Starting phenix.real_space_refine on Mon Jun 16 15:28:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxj_40854/06_2025/8sxj_40854_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxj_40854/06_2025/8sxj_40854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sxj_40854/06_2025/8sxj_40854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxj_40854/06_2025/8sxj_40854.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxj_40854/06_2025/8sxj_40854_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxj_40854/06_2025/8sxj_40854_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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 132 5.16 5 C 12003 2.51 5 N 3327 2.21 5 O 3588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19050 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Chain: "B" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "E" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Time building chain proxies: 11.52, per 1000 atoms: 0.60 Number of scatterers: 19050 At special positions: 0 Unit cell: (145.084, 134.596, 117.99, 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 132 16.00 O 3588 8.00 N 3327 7.00 C 12003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS I 167 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS E 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 167 " - pdb=" SG CYS I 127 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.04 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 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: 4.38 Conformation dependent library (CDL) restraints added in 2.4 seconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 37 sheets defined 19.5% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.600A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.614A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.668A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.536A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.682A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.543A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 100 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 353 removed outlier: 4.525A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.503A pdb=" N PHE E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 482 removed outlier: 3.674A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.532A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 546 No H-bonds generated for 'chain 'F' and resid 544 through 546' Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.678A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 100 through 117 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 334 through 353 removed outlier: 4.537A pdb=" N GLU I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 392 removed outlier: 3.508A pdb=" N PHE I 391 " --> pdb=" O THR I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 482 removed outlier: 3.666A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU I 480 " --> pdb=" O ASN I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 543 removed outlier: 3.527A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 544 through 546 No H-bonds generated for 'chain 'J' and resid 544 through 546' Processing helix chain 'J' and resid 572 through 596 removed outlier: 3.678A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) Processing helix chain 'J' and resid 621 through 625 Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 664 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 5.220A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.637A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.434A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 304 removed outlier: 4.275A pdb=" N GLN A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 320 through 323 current: chain 'A' and resid 382 through 385 removed outlier: 3.967A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 414 through 421 current: chain 'A' and resid 466 through 468 Processing sheet with id=AA8, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 361 removed outlier: 3.898A pdb=" N ARG A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 removed outlier: 4.170A pdb=" N SER C 21 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB2, 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 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100B through 103 Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB4, 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 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 54 current: chain 'D' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'E' and resid 493 through 497 removed outlier: 5.217A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.639A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.372A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.761A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 382 through 385 removed outlier: 3.901A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 414 through 421 current: chain 'E' and resid 466 through 468 Processing sheet with id=AC3, first strand: chain 'E' and resid 358 through 361 removed outlier: 3.887A pdb=" N ARG E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.171A pdb=" N SER G 21 " --> pdb=" O TYR G 7 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AC5, 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 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100B through 103 Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 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=AC8, first strand: chain 'I' and resid 493 through 497 removed outlier: 5.223A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.640A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD2, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'I' and resid 170 through 177 Processing sheet with id=AD4, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.045A pdb=" N VAL I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR I 435 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 308 removed outlier: 4.034A pdb=" N GLN I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR I 320 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 316 through 323 current: chain 'I' and resid 382 through 385 removed outlier: 3.900A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 414 through 421 current: chain 'I' and resid 466 through 468 Processing sheet with id=AD6, first strand: chain 'I' and resid 358 through 361 removed outlier: 3.893A pdb=" N ARG I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 7 removed outlier: 4.146A pdb=" N SER K 21 " --> pdb=" O TYR K 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR K 77 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100B through 103 Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 553 hydrogen bonds defined for protein. 1476 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: 6.51 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.52: 12474 1.52 - 1.83: 6982 1.83 - 2.14: 0 2.14 - 2.45: 0 2.45 - 2.76: 2 Bond restraints: 19458 Sorted by residual: bond pdb=" C TRP H 94 " pdb=" N TRP H 96 " ideal model delta sigma weight residual 1.331 2.765 -1.434 1.51e-02 4.39e+03 9.02e+03 bond pdb=" C TRP L 94 " pdb=" N TRP L 96 " ideal model delta sigma weight residual 1.331 2.763 -1.432 1.51e-02 4.39e+03 8.99e+03 bond pdb=" CZ ARG K 66 " pdb=" NH2 ARG K 66 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" CZ ARG G 66 " pdb=" NH2 ARG G 66 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG C 66 " pdb=" NH2 ARG C 66 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.16e+01 ... (remaining 19453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 26228 5.04 - 10.09: 171 10.09 - 15.13: 5 15.13 - 20.18: 0 20.18 - 25.22: 2 Bond angle restraints: 26406 Sorted by residual: angle pdb=" O TRP H 94 " pdb=" C TRP H 94 " pdb=" N TRP H 96 " ideal model delta sigma weight residual 121.20 95.98 25.22 1.61e+00 3.86e-01 2.45e+02 angle pdb=" O TRP L 94 " pdb=" C TRP L 94 " pdb=" N TRP L 96 " ideal model delta sigma weight residual 121.20 96.28 24.92 1.61e+00 3.86e-01 2.40e+02 angle pdb=" C TRP L 94 " pdb=" N TRP L 96 " pdb=" CA TRP L 96 " ideal model delta sigma weight residual 122.62 109.69 12.93 1.56e+00 4.11e-01 6.87e+01 angle pdb=" C TRP H 94 " pdb=" N TRP H 96 " pdb=" CA TRP H 96 " ideal model delta sigma weight residual 122.62 109.91 12.71 1.56e+00 4.11e-01 6.64e+01 angle pdb=" N LYS A 356 " pdb=" CA LYS A 356 " pdb=" C LYS A 356 " ideal model delta sigma weight residual 111.71 119.00 -7.29 1.15e+00 7.56e-01 4.02e+01 ... (remaining 26401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10815 17.97 - 35.95: 689 35.95 - 53.92: 135 53.92 - 71.89: 34 71.89 - 89.86: 24 Dihedral angle restraints: 11697 sinusoidal: 4707 harmonic: 6990 Sorted by residual: dihedral pdb=" CA TRP H 94 " pdb=" C TRP H 94 " pdb=" N TRP H 96 " pdb=" CA TRP H 96 " ideal model delta harmonic sigma weight residual 180.00 122.70 57.30 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA TRP L 94 " pdb=" C TRP L 94 " pdb=" N TRP L 96 " pdb=" CA TRP L 96 " ideal model delta harmonic sigma weight residual 180.00 123.05 56.95 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA ILE E 141 " pdb=" C ILE E 141 " pdb=" N ILE E 142 " pdb=" CA ILE E 142 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 11694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1717 0.078 - 0.155: 987 0.155 - 0.232: 182 0.232 - 0.310: 44 0.310 - 0.387: 7 Chirality restraints: 2937 Sorted by residual: chirality pdb=" CA ARG A 166 " pdb=" N ARG A 166 " pdb=" C ARG A 166 " pdb=" CB ARG A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ALA J 532 " pdb=" N ALA J 532 " pdb=" C ALA J 532 " pdb=" CB ALA J 532 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ALA B 532 " pdb=" N ALA B 532 " pdb=" C ALA B 532 " pdb=" CB ALA B 532 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 2934 not shown) Planarity restraints: 3378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP H 94 " 0.133 2.00e-02 2.50e+03 1.93e-01 3.74e+02 pdb=" C TRP H 94 " -0.329 2.00e-02 2.50e+03 pdb=" O TRP H 94 " 0.147 2.00e-02 2.50e+03 pdb=" N TRP H 96 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 94 " 0.131 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C TRP L 94 " -0.324 2.00e-02 2.50e+03 pdb=" O TRP L 94 " 0.144 2.00e-02 2.50e+03 pdb=" N TRP L 96 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 427 " -0.133 2.00e-02 2.50e+03 6.89e-02 1.19e+02 pdb=" CG TRP E 427 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP E 427 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP E 427 " 0.082 2.00e-02 2.50e+03 pdb=" NE1 TRP E 427 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP E 427 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP E 427 " 0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 427 " -0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 427 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 427 " -0.082 2.00e-02 2.50e+03 ... (remaining 3375 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 10446 3.02 - 3.49: 19002 3.49 - 3.96: 30398 3.96 - 4.43: 32778 4.43 - 4.90: 54776 Nonbonded interactions: 147400 Sorted by model distance: nonbonded pdb=" OE2 GLU I 62 " pdb=" OG1 THR I 77 " model vdw 2.555 3.040 nonbonded pdb=" OE2 GLU A 62 " pdb=" OG1 THR A 77 " model vdw 2.556 3.040 nonbonded pdb=" OE2 GLU E 62 " pdb=" OG1 THR E 77 " model vdw 2.556 3.040 nonbonded pdb=" OG1 THR K 19 " pdb=" OD1 ASP K 81 " model vdw 2.580 3.040 nonbonded pdb=" OE2 GLU I 83 " pdb=" OG SER I 243 " model vdw 2.582 3.040 ... (remaining 147395 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 44.080 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.019 1.434 19500 Z= 1.191 Angle : 1.762 25.222 26490 Z= 1.165 Chirality : 0.094 0.387 2937 Planarity : 0.016 0.193 3378 Dihedral : 13.378 89.863 7083 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.99 % Favored : 92.34 % Rotamer: Outliers : 1.10 % Allowed : 2.62 % Favored : 96.29 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2375 helix: -0.07 (0.25), residues: 339 sheet: -0.31 (0.21), residues: 534 loop : -1.04 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.133 0.030 TRP E 427 HIS 0.016 0.004 HIS A 249 PHE 0.099 0.013 PHE D 71 TYR 0.118 0.022 TYR F 586 ARG 0.013 0.001 ARG I 273 Details of bonding type rmsd hydrogen bonds : bond 0.14817 ( 553) hydrogen bonds : angle 7.34465 ( 1476) SS BOND : bond 0.00720 ( 42) SS BOND : angle 1.51501 ( 84) covalent geometry : bond 0.01882 (19458) covalent geometry : angle 1.76286 (26406) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 550 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8084 (m100) cc_final: 0.7851 (m-10) REVERT: A 178 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8407 (tmtt) REVERT: B 538 THR cc_start: 0.8702 (p) cc_final: 0.8494 (p) REVERT: B 575 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: C 75 MET cc_start: 0.7711 (mmm) cc_final: 0.7450 (mtp) REVERT: E 178 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8294 (tmtt) REVERT: E 396 MET cc_start: 0.8988 (pmm) cc_final: 0.7216 (mtt) REVERT: F 538 THR cc_start: 0.8745 (p) cc_final: 0.8480 (p) REVERT: F 575 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: G 18 MET cc_start: 0.8393 (ptt) cc_final: 0.8166 (ptp) REVERT: G 75 MET cc_start: 0.7601 (mmm) cc_final: 0.7264 (mtp) REVERT: I 35 TRP cc_start: 0.8142 (m100) cc_final: 0.7724 (m-10) REVERT: I 315 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6634 (pt0) REVERT: I 396 MET cc_start: 0.8884 (pmm) cc_final: 0.7267 (mtt) REVERT: J 538 THR cc_start: 0.8857 (p) cc_final: 0.8529 (p) REVERT: J 575 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6212 (tt0) REVERT: J 647 GLU cc_start: 0.7417 (tt0) cc_final: 0.6881 (tt0) REVERT: K 75 MET cc_start: 0.7706 (mmm) cc_final: 0.7268 (mtp) REVERT: L 5 THR cc_start: 0.7812 (m) cc_final: 0.7477 (p) REVERT: L 46 LEU cc_start: 0.7935 (tp) cc_final: 0.7690 (pt) outliers start: 23 outliers final: 6 residues processed: 573 average time/residue: 0.3754 time to fit residues: 307.2502 Evaluate side-chains 349 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 339 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain J residue 575 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 195 ASN A 262 ASN A 334 ASN A 425 ASN D 37 GLN D 38 HIS E 72 HIS E 105 HIS H 37 GLN H 38 HIS I 72 HIS I 334 ASN L 37 GLN L 38 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.165778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.139888 restraints weight = 23028.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139784 restraints weight = 22327.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139771 restraints weight = 21944.125| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19500 Z= 0.156 Angle : 0.763 12.825 26490 Z= 0.406 Chirality : 0.048 0.216 2937 Planarity : 0.005 0.044 3378 Dihedral : 7.826 89.701 2652 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.20 % Favored : 95.54 % Rotamer: Outliers : 2.90 % Allowed : 11.67 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2379 helix: 1.61 (0.27), residues: 363 sheet: -0.41 (0.19), residues: 660 loop : -0.99 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 96 HIS 0.010 0.002 HIS I 249 PHE 0.016 0.002 PHE L 98 TYR 0.021 0.002 TYR A 177 ARG 0.005 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 553) hydrogen bonds : angle 5.44060 ( 1476) SS BOND : bond 0.00422 ( 42) SS BOND : angle 1.94699 ( 84) covalent geometry : bond 0.00336 (19458) covalent geometry : angle 0.75622 (26406) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 354 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8207 (m100) cc_final: 0.7986 (m100) REVERT: A 396 MET cc_start: 0.8973 (pmm) cc_final: 0.7434 (mtt) REVERT: E 170 GLU cc_start: 0.7242 (tt0) cc_final: 0.6954 (mt-10) REVERT: E 275 GLU cc_start: 0.7706 (tp30) cc_final: 0.7461 (tp30) REVERT: E 396 MET cc_start: 0.8811 (pmm) cc_final: 0.7526 (mtt) REVERT: E 426 MET cc_start: 0.7967 (mtt) cc_final: 0.7538 (mmt) REVERT: G 39 GLN cc_start: 0.7784 (tt0) cc_final: 0.7501 (tt0) REVERT: H 100 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8247 (mm-40) REVERT: I 35 TRP cc_start: 0.8234 (m100) cc_final: 0.7702 (m-10) REVERT: I 308 ARG cc_start: 0.7574 (mtp85) cc_final: 0.6833 (mmp-170) REVERT: I 315 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6974 (pt0) REVERT: I 396 MET cc_start: 0.8781 (pmm) cc_final: 0.7357 (mtt) REVERT: I 434 MET cc_start: 0.7675 (ttp) cc_final: 0.7467 (ttp) outliers start: 61 outliers final: 30 residues processed: 393 average time/residue: 0.3296 time to fit residues: 195.6716 Evaluate side-chains 323 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 246 GLN B 607 ASN E 72 HIS E 246 GLN E 300 ASN H 37 GLN I 72 HIS I 105 HIS I 246 GLN J 658 GLN L 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.157182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.137504 restraints weight = 23900.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.129570 restraints weight = 36936.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.128115 restraints weight = 28939.282| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19500 Z= 0.247 Angle : 0.767 12.980 26490 Z= 0.410 Chirality : 0.049 0.229 2937 Planarity : 0.005 0.045 3378 Dihedral : 6.535 60.677 2643 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.80 % Favored : 93.95 % Rotamer: Outliers : 4.10 % Allowed : 13.81 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2379 helix: 1.30 (0.28), residues: 381 sheet: -0.57 (0.19), residues: 693 loop : -1.03 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 35 HIS 0.010 0.002 HIS E 249 PHE 0.017 0.002 PHE I 361 TYR 0.029 0.003 TYR E 482 ARG 0.007 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 553) hydrogen bonds : angle 5.27884 ( 1476) SS BOND : bond 0.00777 ( 42) SS BOND : angle 1.59424 ( 84) covalent geometry : bond 0.00575 (19458) covalent geometry : angle 0.76280 (26406) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 353 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8313 (m100) cc_final: 0.7793 (m-10) REVERT: A 49 LYS cc_start: 0.8545 (mptt) cc_final: 0.8251 (ptmm) REVERT: A 178 LYS cc_start: 0.8529 (tmtt) cc_final: 0.8041 (mtmm) REVERT: A 207 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7918 (ptmm) REVERT: A 246 GLN cc_start: 0.7030 (mp10) cc_final: 0.6485 (mm-40) REVERT: A 396 MET cc_start: 0.8899 (pmm) cc_final: 0.7221 (mtt) REVERT: A 426 MET cc_start: 0.8514 (mtt) cc_final: 0.8184 (mtp) REVERT: A 434 MET cc_start: 0.7912 (ptm) cc_final: 0.7609 (ptm) REVERT: A 498 ARG cc_start: 0.7418 (ttm110) cc_final: 0.6575 (tpt-90) REVERT: B 617 ARG cc_start: 0.8154 (mmt-90) cc_final: 0.5407 (ttp-170) REVERT: E 170 GLU cc_start: 0.7498 (tt0) cc_final: 0.7176 (mt-10) REVERT: E 275 GLU cc_start: 0.8062 (tp30) cc_final: 0.7659 (tp30) REVERT: E 290 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8057 (tm-30) REVERT: E 396 MET cc_start: 0.8872 (pmm) cc_final: 0.7361 (mtt) REVERT: E 458 TYR cc_start: 0.8277 (t80) cc_final: 0.7865 (t80) REVERT: F 626 MET cc_start: 0.6862 (tpt) cc_final: 0.6660 (tpt) REVERT: G 39 GLN cc_start: 0.8216 (tt0) cc_final: 0.7972 (tt0) REVERT: I 290 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8024 (tm-30) REVERT: I 315 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7299 (pt0) REVERT: I 396 MET cc_start: 0.8918 (pmm) cc_final: 0.7422 (mtt) REVERT: I 426 MET cc_start: 0.8411 (mtt) cc_final: 0.8169 (mtt) REVERT: J 530 MET cc_start: 0.7287 (mmt) cc_final: 0.6886 (mmm) REVERT: J 540 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7260 (tm-30) REVERT: J 634 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8042 (mt-10) REVERT: K 39 GLN cc_start: 0.8261 (tt0) cc_final: 0.8014 (tt0) outliers start: 86 outliers final: 53 residues processed: 399 average time/residue: 0.3224 time to fit residues: 193.1213 Evaluate side-chains 359 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 304 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 159 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 425 ASN B 607 ASN B 625 ASN B 658 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 625 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.161143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.131763 restraints weight = 23922.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.131761 restraints weight = 23228.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.131760 restraints weight = 23219.812| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19500 Z= 0.140 Angle : 0.662 12.734 26490 Z= 0.351 Chirality : 0.045 0.208 2937 Planarity : 0.004 0.049 3378 Dihedral : 6.116 61.273 2643 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.96 % Favored : 94.79 % Rotamer: Outliers : 3.24 % Allowed : 16.14 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2379 helix: 1.93 (0.28), residues: 360 sheet: -0.50 (0.18), residues: 738 loop : -0.89 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 35 HIS 0.008 0.001 HIS I 249 PHE 0.010 0.001 PHE H 71 TYR 0.019 0.002 TYR H 91 ARG 0.005 0.000 ARG F 542 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 553) hydrogen bonds : angle 5.06783 ( 1476) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.43503 ( 84) covalent geometry : bond 0.00320 (19458) covalent geometry : angle 0.65837 (26406) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 327 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8242 (m100) cc_final: 0.7837 (m-10) REVERT: A 49 LYS cc_start: 0.8461 (mptt) cc_final: 0.8245 (ptmm) REVERT: A 178 LYS cc_start: 0.8359 (tmtt) cc_final: 0.8080 (mtmm) REVERT: A 207 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7845 (ptmt) REVERT: A 246 GLN cc_start: 0.7060 (mp10) cc_final: 0.6704 (mm-40) REVERT: A 396 MET cc_start: 0.8793 (pmm) cc_final: 0.7376 (mtt) REVERT: A 434 MET cc_start: 0.7839 (ptm) cc_final: 0.7628 (ptm) REVERT: B 617 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.5599 (ttp-170) REVERT: E 49 LYS cc_start: 0.8380 (mptt) cc_final: 0.8063 (mttp) REVERT: E 67 ASN cc_start: 0.8087 (t0) cc_final: 0.7725 (t0) REVERT: E 246 GLN cc_start: 0.6899 (mp10) cc_final: 0.6598 (tp-100) REVERT: E 302 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7779 (mmtm) REVERT: E 396 MET cc_start: 0.8765 (pmm) cc_final: 0.7493 (mtt) REVERT: E 458 TYR cc_start: 0.8267 (t80) cc_final: 0.7851 (t80) REVERT: G 39 GLN cc_start: 0.8123 (tt0) cc_final: 0.7877 (tt0) REVERT: I 114 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7068 (mt0) REVERT: I 208 LEU cc_start: 0.7443 (mp) cc_final: 0.7240 (mt) REVERT: I 315 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7140 (pt0) REVERT: I 396 MET cc_start: 0.8837 (pmm) cc_final: 0.7522 (mtt) REVERT: J 540 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7286 (tm-30) REVERT: J 635 ILE cc_start: 0.8468 (mm) cc_final: 0.8182 (mm) REVERT: K 39 GLN cc_start: 0.8120 (tt0) cc_final: 0.7902 (tt0) REVERT: K 75 MET cc_start: 0.8101 (mtp) cc_final: 0.7890 (mtp) outliers start: 68 outliers final: 41 residues processed: 371 average time/residue: 0.3204 time to fit residues: 179.3832 Evaluate side-chains 349 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 26 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN I 72 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 ASN J 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.160887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.139276 restraints weight = 23921.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.136669 restraints weight = 41056.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134937 restraints weight = 42552.165| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19500 Z= 0.140 Angle : 0.627 12.509 26490 Z= 0.332 Chirality : 0.045 0.202 2937 Planarity : 0.004 0.049 3378 Dihedral : 5.809 61.215 2641 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 3.29 % Allowed : 17.48 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2379 helix: 2.08 (0.28), residues: 360 sheet: -0.38 (0.19), residues: 702 loop : -0.93 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 35 HIS 0.008 0.001 HIS I 355 PHE 0.010 0.001 PHE H 71 TYR 0.018 0.002 TYR H 91 ARG 0.006 0.000 ARG J 542 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 553) hydrogen bonds : angle 5.00585 ( 1476) SS BOND : bond 0.00602 ( 42) SS BOND : angle 1.43890 ( 84) covalent geometry : bond 0.00313 (19458) covalent geometry : angle 0.62256 (26406) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 325 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8223 (m100) cc_final: 0.7896 (m-10) REVERT: A 246 GLN cc_start: 0.6903 (mp10) cc_final: 0.6677 (tp-100) REVERT: A 396 MET cc_start: 0.8762 (pmm) cc_final: 0.7503 (mtt) REVERT: A 426 MET cc_start: 0.8494 (mtp) cc_final: 0.7898 (mtp) REVERT: A 434 MET cc_start: 0.7864 (ptm) cc_final: 0.7592 (ptm) REVERT: B 617 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.5689 (ttp-170) REVERT: E 49 LYS cc_start: 0.8363 (mptt) cc_final: 0.7973 (ptmm) REVERT: E 67 ASN cc_start: 0.8032 (t0) cc_final: 0.7678 (t0) REVERT: E 114 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7091 (mt0) REVERT: E 396 MET cc_start: 0.8751 (pmm) cc_final: 0.7576 (mtt) REVERT: F 628 TRP cc_start: 0.7991 (m100) cc_final: 0.7778 (m100) REVERT: G 39 GLN cc_start: 0.8137 (tt0) cc_final: 0.7906 (tt0) REVERT: I 114 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7299 (mt0) REVERT: I 308 ARG cc_start: 0.7745 (mtp85) cc_final: 0.6990 (mmp-170) REVERT: I 396 MET cc_start: 0.8791 (pmm) cc_final: 0.7573 (mtt) REVERT: J 617 ARG cc_start: 0.7986 (mmt-90) cc_final: 0.5527 (ttp-170) REVERT: J 635 ILE cc_start: 0.8485 (mm) cc_final: 0.8144 (mm) REVERT: K 39 GLN cc_start: 0.8146 (tt0) cc_final: 0.7915 (tt0) REVERT: K 75 MET cc_start: 0.8114 (mtp) cc_final: 0.7865 (mtp) outliers start: 69 outliers final: 46 residues processed: 365 average time/residue: 0.3066 time to fit residues: 170.3452 Evaluate side-chains 347 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 149 optimal weight: 0.0970 chunk 201 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN D 37 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN I 72 HIS I 195 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN J 607 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.158029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.137327 restraints weight = 24004.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.134953 restraints weight = 41737.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.133281 restraints weight = 43939.720| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19500 Z= 0.187 Angle : 0.654 12.645 26490 Z= 0.347 Chirality : 0.045 0.212 2937 Planarity : 0.004 0.060 3378 Dihedral : 5.554 28.928 2637 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 4.19 % Allowed : 17.33 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2379 helix: 1.94 (0.28), residues: 363 sheet: -0.36 (0.19), residues: 696 loop : -0.98 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 35 HIS 0.008 0.002 HIS I 355 PHE 0.013 0.002 PHE E 361 TYR 0.019 0.002 TYR K 7 ARG 0.005 0.000 ARG J 542 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 553) hydrogen bonds : angle 5.05523 ( 1476) SS BOND : bond 0.00590 ( 42) SS BOND : angle 1.43885 ( 84) covalent geometry : bond 0.00438 (19458) covalent geometry : angle 0.64994 (26406) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 324 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8241 (m100) cc_final: 0.7733 (m-10) REVERT: A 50 THR cc_start: 0.8597 (t) cc_final: 0.8384 (m) REVERT: A 114 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7216 (mt0) REVERT: A 246 GLN cc_start: 0.7077 (mp10) cc_final: 0.6741 (tp-100) REVERT: A 396 MET cc_start: 0.8662 (pmm) cc_final: 0.7461 (mtt) REVERT: B 617 ARG cc_start: 0.8296 (mmt-90) cc_final: 0.5655 (ttp-170) REVERT: E 49 LYS cc_start: 0.8243 (mptt) cc_final: 0.7953 (ptmm) REVERT: E 67 ASN cc_start: 0.8024 (t0) cc_final: 0.7741 (t0) REVERT: E 114 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7090 (mt0) REVERT: E 178 LYS cc_start: 0.8145 (tmtt) cc_final: 0.7917 (mtmm) REVERT: E 198 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8751 (t) REVERT: E 207 LYS cc_start: 0.8185 (ptmm) cc_final: 0.7968 (ptmm) REVERT: E 396 MET cc_start: 0.8760 (pmm) cc_final: 0.7656 (mtt) REVERT: E 426 MET cc_start: 0.8457 (mmt) cc_final: 0.8244 (mmt) REVERT: F 628 TRP cc_start: 0.8152 (m100) cc_final: 0.7948 (m100) REVERT: G 39 GLN cc_start: 0.8257 (tt0) cc_final: 0.7874 (tt0) REVERT: H 90 GLN cc_start: 0.9329 (pp30) cc_final: 0.8949 (pp30) REVERT: I 50 THR cc_start: 0.8617 (t) cc_final: 0.8350 (m) REVERT: I 72 HIS cc_start: 0.4121 (t70) cc_final: 0.3901 (t-90) REVERT: I 114 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7222 (mt0) REVERT: I 396 MET cc_start: 0.8806 (pmm) cc_final: 0.7585 (mtt) REVERT: J 540 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7384 (tm-30) REVERT: J 617 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.5530 (ttp-170) REVERT: J 630 GLN cc_start: 0.8773 (mp10) cc_final: 0.8548 (mt0) REVERT: K 39 GLN cc_start: 0.8274 (tt0) cc_final: 0.8050 (tt0) REVERT: K 75 MET cc_start: 0.8153 (mtp) cc_final: 0.7856 (mtp) REVERT: L 90 GLN cc_start: 0.9343 (pp30) cc_final: 0.9035 (pp30) outliers start: 88 outliers final: 60 residues processed: 373 average time/residue: 0.3035 time to fit residues: 174.1340 Evaluate side-chains 373 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 312 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 144 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 181 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 HIS ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.161700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.140434 restraints weight = 23677.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.138036 restraints weight = 39427.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.137890 restraints weight = 41601.533| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19500 Z= 0.114 Angle : 0.606 12.287 26490 Z= 0.320 Chirality : 0.043 0.211 2937 Planarity : 0.004 0.051 3378 Dihedral : 5.278 26.505 2637 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 3.52 % Allowed : 17.81 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2379 helix: 2.26 (0.29), residues: 363 sheet: -0.16 (0.20), residues: 666 loop : -0.96 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 35 HIS 0.008 0.001 HIS I 355 PHE 0.010 0.001 PHE J 522 TYR 0.022 0.001 TYR K 7 ARG 0.004 0.000 ARG J 542 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 553) hydrogen bonds : angle 4.96207 ( 1476) SS BOND : bond 0.00406 ( 42) SS BOND : angle 1.36113 ( 84) covalent geometry : bond 0.00254 (19458) covalent geometry : angle 0.60233 (26406) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 323 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8181 (m100) cc_final: 0.7750 (m-10) REVERT: A 50 THR cc_start: 0.8618 (t) cc_final: 0.8412 (m) REVERT: A 114 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7291 (mt0) REVERT: A 246 GLN cc_start: 0.6985 (mp10) cc_final: 0.6708 (tp-100) REVERT: A 396 MET cc_start: 0.8624 (pmm) cc_final: 0.7491 (mtt) REVERT: A 426 MET cc_start: 0.8422 (mtp) cc_final: 0.7968 (mmm) REVERT: B 537 LEU cc_start: 0.8708 (mt) cc_final: 0.8432 (mt) REVERT: B 617 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.5621 (ttp-170) REVERT: E 49 LYS cc_start: 0.8109 (mptt) cc_final: 0.7864 (ptmm) REVERT: E 67 ASN cc_start: 0.7966 (t0) cc_final: 0.7715 (t0) REVERT: E 114 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7106 (mt0) REVERT: E 178 LYS cc_start: 0.8022 (tmtt) cc_final: 0.7820 (mtmm) REVERT: E 198 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8736 (t) REVERT: E 207 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7876 (ptmm) REVERT: E 396 MET cc_start: 0.8690 (pmm) cc_final: 0.7633 (mtt) REVERT: F 537 LEU cc_start: 0.8579 (mt) cc_final: 0.8339 (mt) REVERT: G 39 GLN cc_start: 0.8208 (tt0) cc_final: 0.7839 (tt0) REVERT: G 71 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7656 (pmt-80) REVERT: H 90 GLN cc_start: 0.9297 (pp30) cc_final: 0.8937 (pp30) REVERT: I 35 TRP cc_start: 0.8133 (m100) cc_final: 0.7393 (m-10) REVERT: I 50 THR cc_start: 0.8502 (t) cc_final: 0.8247 (m) REVERT: I 114 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7376 (mt0) REVERT: I 178 LYS cc_start: 0.8352 (mtpt) cc_final: 0.7811 (mtmm) REVERT: I 308 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7258 (mpt180) REVERT: I 396 MET cc_start: 0.8766 (pmm) cc_final: 0.7581 (mtt) REVERT: J 617 ARG cc_start: 0.7979 (mmt-90) cc_final: 0.5696 (ttp-110) REVERT: J 630 GLN cc_start: 0.8738 (mp10) cc_final: 0.8491 (mt0) REVERT: K 39 GLN cc_start: 0.8244 (tt0) cc_final: 0.8013 (tt0) REVERT: L 90 GLN cc_start: 0.9296 (pp30) cc_final: 0.8907 (pp30) outliers start: 74 outliers final: 53 residues processed: 364 average time/residue: 0.3163 time to fit residues: 175.9500 Evaluate side-chains 361 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 186 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.158665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.137852 restraints weight = 24004.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.135683 restraints weight = 39159.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.135001 restraints weight = 41820.181| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19500 Z= 0.178 Angle : 0.647 12.647 26490 Z= 0.338 Chirality : 0.045 0.212 2937 Planarity : 0.004 0.059 3378 Dihedral : 5.316 26.704 2637 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 3.33 % Allowed : 18.76 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2379 helix: 2.11 (0.28), residues: 363 sheet: -0.23 (0.20), residues: 678 loop : -0.98 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 35 HIS 0.009 0.002 HIS I 355 PHE 0.012 0.002 PHE I 361 TYR 0.017 0.002 TYR K 7 ARG 0.004 0.000 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 553) hydrogen bonds : angle 5.00447 ( 1476) SS BOND : bond 0.00422 ( 42) SS BOND : angle 1.48369 ( 84) covalent geometry : bond 0.00419 (19458) covalent geometry : angle 0.64309 (26406) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 313 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8201 (m100) cc_final: 0.7685 (m-10) REVERT: A 114 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7187 (mt0) REVERT: A 246 GLN cc_start: 0.7106 (mp10) cc_final: 0.6829 (tp-100) REVERT: A 396 MET cc_start: 0.8589 (pmm) cc_final: 0.7544 (mtt) REVERT: A 443 ILE cc_start: 0.7898 (tp) cc_final: 0.7695 (mm) REVERT: B 617 ARG cc_start: 0.8311 (mmt-90) cc_final: 0.5631 (ttp-170) REVERT: C 71 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7889 (pmt-80) REVERT: E 49 LYS cc_start: 0.8163 (mptt) cc_final: 0.7897 (ptmm) REVERT: E 67 ASN cc_start: 0.8012 (t0) cc_final: 0.7793 (t0) REVERT: E 114 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7139 (mt0) REVERT: E 198 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8654 (t) REVERT: E 207 LYS cc_start: 0.8270 (ptmm) cc_final: 0.8041 (ptmm) REVERT: E 396 MET cc_start: 0.8684 (pmm) cc_final: 0.7733 (mtt) REVERT: E 500 LYS cc_start: 0.7671 (ttpt) cc_final: 0.7353 (ttpt) REVERT: F 537 LEU cc_start: 0.8596 (mt) cc_final: 0.8379 (mt) REVERT: F 617 ARG cc_start: 0.8050 (mmt-90) cc_final: 0.5341 (ttp-170) REVERT: G 6 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: G 39 GLN cc_start: 0.8222 (tt0) cc_final: 0.7837 (tt0) REVERT: G 71 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7798 (pmt-80) REVERT: H 90 GLN cc_start: 0.9352 (pp30) cc_final: 0.8932 (pp30) REVERT: I 50 THR cc_start: 0.8547 (t) cc_final: 0.8296 (m) REVERT: I 114 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7384 (mt0) REVERT: I 178 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7845 (mtmm) REVERT: I 396 MET cc_start: 0.8756 (pmm) cc_final: 0.7652 (mtt) REVERT: J 617 ARG cc_start: 0.7998 (mmt-90) cc_final: 0.4861 (ttp-170) REVERT: K 6 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: K 39 GLN cc_start: 0.8284 (tt0) cc_final: 0.8020 (tt0) REVERT: K 75 MET cc_start: 0.8104 (mtp) cc_final: 0.7787 (mtm) REVERT: L 90 GLN cc_start: 0.9370 (pp30) cc_final: 0.9083 (pp30) outliers start: 70 outliers final: 55 residues processed: 351 average time/residue: 0.3180 time to fit residues: 169.2391 Evaluate side-chains 362 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 169 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 206 optimal weight: 0.0010 chunk 95 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN J 651 ASN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.138443 restraints weight = 24055.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.136346 restraints weight = 39626.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.135329 restraints weight = 42032.121| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19500 Z= 0.148 Angle : 0.630 12.551 26490 Z= 0.329 Chirality : 0.044 0.252 2937 Planarity : 0.004 0.053 3378 Dihedral : 5.266 26.699 2637 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 3.19 % Allowed : 19.38 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2379 helix: 2.17 (0.28), residues: 363 sheet: -0.22 (0.20), residues: 678 loop : -0.97 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP E 35 HIS 0.009 0.002 HIS I 355 PHE 0.010 0.001 PHE I 361 TYR 0.021 0.002 TYR K 7 ARG 0.004 0.000 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 553) hydrogen bonds : angle 4.98515 ( 1476) SS BOND : bond 0.00482 ( 42) SS BOND : angle 1.46709 ( 84) covalent geometry : bond 0.00346 (19458) covalent geometry : angle 0.62570 (26406) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 314 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8190 (m100) cc_final: 0.7590 (m-10) REVERT: A 114 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7209 (mt0) REVERT: A 246 GLN cc_start: 0.7120 (mp10) cc_final: 0.6806 (tp-100) REVERT: A 396 MET cc_start: 0.8508 (pmm) cc_final: 0.7527 (mtt) REVERT: A 443 ILE cc_start: 0.7896 (tp) cc_final: 0.7649 (mm) REVERT: B 617 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.5550 (ttp-170) REVERT: C 71 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7799 (pmt-80) REVERT: E 35 TRP cc_start: 0.8001 (m-10) cc_final: 0.7789 (m-10) REVERT: E 49 LYS cc_start: 0.8110 (mptt) cc_final: 0.7876 (ptmm) REVERT: E 114 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7157 (mt0) REVERT: E 198 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8702 (t) REVERT: E 308 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7230 (mmt180) REVERT: E 396 MET cc_start: 0.8670 (pmm) cc_final: 0.7724 (mtt) REVERT: F 537 LEU cc_start: 0.8609 (mt) cc_final: 0.8355 (mt) REVERT: F 617 ARG cc_start: 0.8064 (mmt-90) cc_final: 0.5297 (ttp-170) REVERT: G 6 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: G 39 GLN cc_start: 0.8218 (tt0) cc_final: 0.7832 (tt0) REVERT: G 71 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7765 (pmt-80) REVERT: H 90 GLN cc_start: 0.9361 (pp30) cc_final: 0.8958 (pp30) REVERT: I 35 TRP cc_start: 0.8182 (m100) cc_final: 0.7444 (m-10) REVERT: I 50 THR cc_start: 0.8506 (t) cc_final: 0.8257 (m) REVERT: I 114 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7361 (mt0) REVERT: I 178 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7806 (mtmm) REVERT: I 396 MET cc_start: 0.8743 (pmm) cc_final: 0.7640 (mtt) REVERT: I 426 MET cc_start: 0.8335 (mtt) cc_final: 0.8130 (mtt) REVERT: J 617 ARG cc_start: 0.7383 (mmt-90) cc_final: 0.5160 (ttp-170) REVERT: K 39 GLN cc_start: 0.8298 (tt0) cc_final: 0.8023 (tt0) REVERT: L 32 ASN cc_start: 0.8563 (m110) cc_final: 0.8310 (m110) REVERT: L 90 GLN cc_start: 0.9380 (pp30) cc_final: 0.9096 (pp30) outliers start: 67 outliers final: 57 residues processed: 351 average time/residue: 0.3175 time to fit residues: 168.9052 Evaluate side-chains 366 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 305 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 223 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 146 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 0.0040 chunk 148 optimal weight: 1.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN D 37 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN J 651 ASN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.160850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.139988 restraints weight = 23921.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.138638 restraints weight = 40605.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.131974 restraints weight = 41096.836| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19500 Z= 0.134 Angle : 0.627 12.404 26490 Z= 0.326 Chirality : 0.044 0.246 2937 Planarity : 0.004 0.052 3378 Dihedral : 5.235 26.529 2637 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.46 % Favored : 94.49 % Rotamer: Outliers : 3.33 % Allowed : 19.43 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2379 helix: 2.25 (0.29), residues: 363 sheet: -0.19 (0.20), residues: 678 loop : -0.96 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.001 TRP E 35 HIS 0.009 0.001 HIS I 355 PHE 0.009 0.001 PHE J 522 TYR 0.020 0.002 TYR K 7 ARG 0.005 0.000 ARG E 502 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 553) hydrogen bonds : angle 4.96607 ( 1476) SS BOND : bond 0.00396 ( 42) SS BOND : angle 1.38735 ( 84) covalent geometry : bond 0.00309 (19458) covalent geometry : angle 0.62262 (26406) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 307 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8207 (m100) cc_final: 0.7395 (m-10) REVERT: A 114 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7353 (mt0) REVERT: A 246 GLN cc_start: 0.7248 (mp10) cc_final: 0.6753 (tp-100) REVERT: A 396 MET cc_start: 0.8430 (pmm) cc_final: 0.7297 (mtt) REVERT: B 617 ARG cc_start: 0.8447 (mmt-90) cc_final: 0.5362 (ttp-170) REVERT: C 71 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7779 (pmt-80) REVERT: E 49 LYS cc_start: 0.8122 (mptt) cc_final: 0.7844 (ptmm) REVERT: E 114 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7408 (mt0) REVERT: E 308 ARG cc_start: 0.8165 (mtp180) cc_final: 0.7233 (mmt180) REVERT: E 396 MET cc_start: 0.8719 (pmm) cc_final: 0.7513 (mtt) REVERT: F 537 LEU cc_start: 0.8604 (mt) cc_final: 0.8374 (mt) REVERT: F 617 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.5047 (ttp-170) REVERT: G 39 GLN cc_start: 0.8309 (tt0) cc_final: 0.7876 (tt0) REVERT: G 71 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7740 (pmt-80) REVERT: H 90 GLN cc_start: 0.9366 (pp30) cc_final: 0.8916 (pp30) REVERT: I 35 TRP cc_start: 0.8187 (m100) cc_final: 0.7248 (m-10) REVERT: I 114 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7268 (mt0) REVERT: I 178 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7801 (mtmm) REVERT: I 396 MET cc_start: 0.8840 (pmm) cc_final: 0.7530 (mtt) REVERT: I 426 MET cc_start: 0.8383 (mtt) cc_final: 0.7549 (mmt) REVERT: J 617 ARG cc_start: 0.7542 (mmt-90) cc_final: 0.5129 (ttp-110) REVERT: K 39 GLN cc_start: 0.8377 (tt0) cc_final: 0.8087 (tt0) REVERT: L 32 ASN cc_start: 0.8605 (m110) cc_final: 0.8362 (m110) REVERT: L 90 GLN cc_start: 0.9367 (pp30) cc_final: 0.9040 (pp30) outliers start: 70 outliers final: 59 residues processed: 344 average time/residue: 0.3593 time to fit residues: 190.7632 Evaluate side-chains 363 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 CYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 229 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.0870 chunk 101 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 226 optimal weight: 0.4980 chunk 172 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 153 optimal weight: 0.0020 overall best weight: 1.7170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN E 216 HIS ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN L 32 ASN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.159972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3381 r_free = 0.3381 target = 0.134147 restraints weight = 23643.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.132911 restraints weight = 30360.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.132895 restraints weight = 32924.164| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19500 Z= 0.157 Angle : 0.635 12.442 26490 Z= 0.331 Chirality : 0.044 0.243 2937 Planarity : 0.004 0.053 3378 Dihedral : 5.261 26.438 2637 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 3.19 % Allowed : 19.57 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2379 helix: 2.23 (0.28), residues: 363 sheet: -0.21 (0.20), residues: 678 loop : -0.98 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP E 35 HIS 0.010 0.002 HIS I 355 PHE 0.011 0.001 PHE I 361 TYR 0.019 0.002 TYR K 7 ARG 0.004 0.000 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 553) hydrogen bonds : angle 4.99381 ( 1476) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.37180 ( 84) covalent geometry : bond 0.00368 (19458) covalent geometry : angle 0.63157 (26406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6128.66 seconds wall clock time: 107 minutes 28.84 seconds (6448.84 seconds total)