Starting phenix.real_space_refine on Mon May 19 17:35:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxj_40854/05_2025/8sxj_40854_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxj_40854/05_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_40854/05_2025/8sxj_40854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxj_40854/05_2025/8sxj_40854.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxj_40854/05_2025/8sxj_40854_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxj_40854/05_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-5687/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: 11.42, 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: 4.26 Conformation dependent library (CDL) restraints added in 2.2 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: 2.82 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: 5.85 Time building geometry restraints manager: 5.03 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 1.740 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.750 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.360 ------------------------------------------------------------------------------- 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 : 2.199 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: 0.3547 time to fit residues: 290.9615 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 : 1.949 ------------------------------------------------------------------------------- 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 = 0.165792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.139921 restraints weight = 23057.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.139491 restraints weight = 23335.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.139490 restraints weight = 22872.999| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 89.702 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 5.44064 ( 1476) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.94715 ( 84) covalent geometry : bond 0.00336 (19458) covalent geometry : angle 0.75623 (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 : 1.913 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: 0.8210 (m100) cc_final: 0.7989 (m100) REVERT: A 396 MET cc_start: 0.8972 (pmm) cc_final: 0.7437 (mtt) REVERT: E 170 GLU cc_start: 0.7235 (tt0) cc_final: 0.6969 (mt-10) REVERT: E 275 GLU cc_start: 0.7698 (tp30) cc_final: 0.7460 (tp30) REVERT: E 396 MET cc_start: 0.8802 (pmm) cc_final: 0.7521 (mtt) REVERT: E 426 MET cc_start: 0.7973 (mtt) cc_final: 0.7548 (mmt) REVERT: G 39 GLN cc_start: 0.7791 (tt0) cc_final: 0.7508 (tt0) REVERT: H 100 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8248 (mm-40) REVERT: I 35 TRP cc_start: 0.8236 (m100) cc_final: 0.7703 (m-10) REVERT: I 308 ARG cc_start: 0.7578 (mtp85) cc_final: 0.6843 (mmp-170) REVERT: I 315 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6993 (pt0) REVERT: I 396 MET cc_start: 0.8779 (pmm) cc_final: 0.7357 (mtt) REVERT: I 434 MET cc_start: 0.7676 (ttp) cc_final: 0.7468 (ttp) outliers start: 61 outliers final: 30 residues processed: 393 average time/residue: 0.3036 time to fit residues: 179.8206 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 : 1.914 ------------------------------------------------------------------------------- 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: 8.9990 chunk 221 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 B 658 GLN E 72 HIS E 246 GLN E 300 ASN H 37 GLN I 72 HIS I 105 HIS I 246 GLN J 658 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.154183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.134161 restraints weight = 24173.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.132428 restraints weight = 36461.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.123428 restraints weight = 38938.119| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 19500 Z= 0.327 Angle : 0.843 13.135 26490 Z= 0.449 Chirality : 0.052 0.225 2937 Planarity : 0.005 0.047 3378 Dihedral : 6.782 63.794 2643 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.93 % Favored : 93.82 % Rotamer: Outliers : 4.43 % Allowed : 14.29 % Favored : 81.29 % 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: -1.05 (0.16), residues: 2379 helix: 1.01 (0.27), residues: 381 sheet: -0.84 (0.18), residues: 723 loop : -1.11 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 35 HIS 0.010 0.002 HIS E 249 PHE 0.023 0.003 PHE I 361 TYR 0.027 0.003 TYR E 482 ARG 0.008 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 553) hydrogen bonds : angle 5.51248 ( 1476) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.63778 ( 84) covalent geometry : bond 0.00782 (19458) covalent geometry : angle 0.83972 (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 457 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 364 time to evaluate : 1.936 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: 0.8341 (m100) cc_final: 0.7687 (m-10) REVERT: A 49 LYS cc_start: 0.8563 (mptt) cc_final: 0.8278 (ptmm) REVERT: A 178 LYS cc_start: 0.8562 (tmtt) cc_final: 0.7977 (mtmm) REVERT: A 207 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7991 (ptmm) REVERT: A 246 GLN cc_start: 0.7241 (mp10) cc_final: 0.6622 (mm-40) REVERT: A 396 MET cc_start: 0.8861 (pmm) cc_final: 0.7115 (mtt) REVERT: A 498 ARG cc_start: 0.7506 (ttm110) cc_final: 0.6576 (tpt-90) REVERT: B 540 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7080 (tm-30) REVERT: D 90 GLN cc_start: 0.9354 (pp30) cc_final: 0.9046 (pp30) REVERT: E 170 GLU cc_start: 0.7498 (tt0) cc_final: 0.7005 (mt-10) REVERT: E 246 GLN cc_start: 0.7162 (mp10) cc_final: 0.6677 (tp-100) REVERT: E 275 GLU cc_start: 0.8188 (tp30) cc_final: 0.7741 (tp30) REVERT: E 290 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8075 (tm-30) REVERT: E 318 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: E 396 MET cc_start: 0.8915 (pmm) cc_final: 0.7284 (mtt) REVERT: E 458 TYR cc_start: 0.8317 (t80) cc_final: 0.7893 (t80) REVERT: F 626 MET cc_start: 0.6832 (tpt) cc_final: 0.5999 (tpt) REVERT: G 39 GLN cc_start: 0.8262 (tt0) cc_final: 0.7923 (tt0) REVERT: I 246 GLN cc_start: 0.7106 (mp10) cc_final: 0.6803 (tp-100) REVERT: I 290 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8003 (tm-30) REVERT: I 315 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7250 (pt0) REVERT: I 396 MET cc_start: 0.8979 (pmm) cc_final: 0.7331 (mtt) REVERT: I 426 MET cc_start: 0.8550 (mtt) cc_final: 0.8275 (mtt) REVERT: J 530 MET cc_start: 0.7368 (mmm) cc_final: 0.6979 (mmm) REVERT: J 540 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7260 (tm-30) REVERT: J 634 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8108 (mt-10) REVERT: K 39 GLN cc_start: 0.8355 (tt0) cc_final: 0.8109 (tt0) outliers start: 93 outliers final: 63 residues processed: 413 average time/residue: 0.2990 time to fit residues: 187.2875 Evaluate side-chains 385 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 2.049 ------------------------------------------------------------------------------- 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 109 ILE 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 B residue 641 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 THR 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 D residue 37 GLN 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 318 TYR Chi-restraints excluded: chain E residue 378 CYS 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 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 H residue 37 GLN Chi-restraints excluded: chain I residue 38 VAL 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 182 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 271 ILE 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 J residue 608 VAL Chi-restraints excluded: chain J residue 641 ILE 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 17 THR 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 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 159 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 175 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 607 ASN B 625 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS F 630 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 625 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.160738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.136910 restraints weight = 23871.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.133655 restraints weight = 39209.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.135019 restraints weight = 40185.886| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3965 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= 0.128 Angle : 0.664 12.706 26490 Z= 0.352 Chirality : 0.045 0.201 2937 Planarity : 0.004 0.048 3378 Dihedral : 6.176 62.457 2643 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.88 % Favored : 94.87 % Rotamer: Outliers : 3.00 % Allowed : 16.57 % Favored : 80.43 % 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: -0.62 (0.17), residues: 2379 helix: 1.57 (0.28), residues: 378 sheet: -0.53 (0.18), residues: 726 loop : -0.91 (0.16), residues: 1275 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 0.027 0.002 TYR E 482 ARG 0.005 0.000 ARG F 542 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 553) hydrogen bonds : angle 5.12540 ( 1476) SS BOND : bond 0.00625 ( 42) SS BOND : angle 1.52203 ( 84) covalent geometry : bond 0.00281 (19458) covalent geometry : angle 0.65963 (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 404 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 341 time to evaluate : 2.108 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: 0.8177 (m100) cc_final: 0.7866 (m-10) REVERT: A 246 GLN cc_start: 0.6948 (mp10) cc_final: 0.6648 (tp-100) REVERT: A 396 MET cc_start: 0.8816 (pmm) cc_final: 0.7439 (mtt) REVERT: A 426 MET cc_start: 0.8311 (mtp) cc_final: 0.8095 (mmm) REVERT: B 617 ARG cc_start: 0.8321 (mmt-90) cc_final: 0.5663 (ttp-170) REVERT: E 49 LYS cc_start: 0.8413 (mptt) cc_final: 0.8064 (mttp) REVERT: E 67 ASN cc_start: 0.8074 (t0) cc_final: 0.7792 (t0) REVERT: E 246 GLN cc_start: 0.6798 (mp10) cc_final: 0.6546 (tp-100) REVERT: E 396 MET cc_start: 0.8792 (pmm) cc_final: 0.7502 (mtt) REVERT: F 628 TRP cc_start: 0.8194 (m100) cc_final: 0.7874 (m100) REVERT: G 39 GLN cc_start: 0.8096 (tt0) cc_final: 0.7858 (tt0) REVERT: H 90 GLN cc_start: 0.9242 (pp30) cc_final: 0.8927 (pp30) REVERT: I 114 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7162 (mt0) REVERT: I 315 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7051 (pt0) REVERT: I 396 MET cc_start: 0.8834 (pmm) cc_final: 0.7562 (mtt) REVERT: J 540 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7298 (tm-30) REVERT: J 635 ILE cc_start: 0.8480 (mm) cc_final: 0.8164 (mm) REVERT: K 39 GLN cc_start: 0.8132 (tt0) cc_final: 0.7891 (tt0) REVERT: K 75 MET cc_start: 0.7995 (mtp) cc_final: 0.7769 (mtp) outliers start: 63 outliers final: 38 residues processed: 381 average time/residue: 0.3071 time to fit residues: 177.2514 Evaluate side-chains 346 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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 125 LEU 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 265 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE 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 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 213 ILE 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 479 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE 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 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: 0.9990 chunk 184 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** A 425 ASN B 607 ASN D 37 GLN ** 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 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.159739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.138507 restraints weight = 23977.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.135963 restraints weight = 37210.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.135620 restraints weight = 39683.654| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19500 Z= 0.144 Angle : 0.639 12.569 26490 Z= 0.337 Chirality : 0.045 0.199 2937 Planarity : 0.004 0.050 3378 Dihedral : 5.863 61.449 2642 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.76 % Favored : 94.12 % Rotamer: Outliers : 3.57 % Allowed : 17.62 % Favored : 78.81 % 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: -0.48 (0.17), residues: 2379 helix: 1.93 (0.28), residues: 363 sheet: -0.35 (0.19), residues: 696 loop : -0.94 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 35 HIS 0.007 0.001 HIS I 355 PHE 0.011 0.001 PHE E 176 TYR 0.018 0.002 TYR H 91 ARG 0.006 0.000 ARG J 542 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 553) hydrogen bonds : angle 5.07270 ( 1476) SS BOND : bond 0.00425 ( 42) SS BOND : angle 1.43533 ( 84) covalent geometry : bond 0.00331 (19458) covalent geometry : angle 0.63458 (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 401 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 326 time to evaluate : 2.017 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: 0.8217 (m100) cc_final: 0.7814 (m-10) REVERT: A 246 GLN cc_start: 0.7001 (mp10) cc_final: 0.6648 (tp-100) REVERT: A 396 MET cc_start: 0.8778 (pmm) cc_final: 0.7437 (mtt) REVERT: B 617 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.5645 (ttp-170) REVERT: C 75 MET cc_start: 0.8244 (mtp) cc_final: 0.7980 (mtm) REVERT: E 49 LYS cc_start: 0.8312 (mptt) cc_final: 0.7908 (ptmm) REVERT: E 50 THR cc_start: 0.8452 (t) cc_final: 0.8236 (m) REVERT: E 67 ASN cc_start: 0.8088 (t0) cc_final: 0.7819 (t0) REVERT: E 396 MET cc_start: 0.8787 (pmm) cc_final: 0.7501 (mtt) REVERT: E 432 ARG cc_start: 0.8037 (tpp-160) cc_final: 0.7826 (ttm-80) REVERT: G 39 GLN cc_start: 0.8191 (tt0) cc_final: 0.7983 (tt0) REVERT: H 90 GLN cc_start: 0.9302 (pp30) cc_final: 0.8925 (pp30) REVERT: I 35 TRP cc_start: 0.8191 (m100) cc_final: 0.7451 (m-10) REVERT: I 114 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7261 (mt0) REVERT: I 308 ARG cc_start: 0.7733 (mtp85) cc_final: 0.6914 (mmp-170) REVERT: I 396 MET cc_start: 0.8817 (pmm) cc_final: 0.7541 (mtt) REVERT: J 540 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7340 (tm-30) REVERT: J 617 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.5478 (ttp-170) REVERT: J 635 ILE cc_start: 0.8501 (mm) cc_final: 0.8187 (mm) REVERT: K 39 GLN cc_start: 0.8254 (tt0) cc_final: 0.7990 (tt0) REVERT: K 75 MET cc_start: 0.8154 (mtp) cc_final: 0.7898 (mtp) REVERT: L 90 GLN cc_start: 0.9290 (pp30) cc_final: 0.9015 (pp30) outliers start: 75 outliers final: 52 residues processed: 377 average time/residue: 0.3023 time to fit residues: 173.5928 Evaluate side-chains 362 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 310 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 450 THR 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 25 SER Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE 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 207 LYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 2 VAL 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 80 MET 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 I residue 479 SER Chi-restraints excluded: chain J residue 651 ASN 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=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: 0.6980 chunk 16 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 B 625 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN 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 625 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.154958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.134592 restraints weight = 24321.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.132977 restraints weight = 37702.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.132780 restraints weight = 41524.229| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19500 Z= 0.245 Angle : 0.709 12.951 26490 Z= 0.376 Chirality : 0.047 0.212 2937 Planarity : 0.005 0.061 3378 Dihedral : 5.741 26.570 2637 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 4.29 % Allowed : 17.81 % 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: -0.68 (0.17), residues: 2379 helix: 1.60 (0.28), residues: 363 sheet: -0.40 (0.20), residues: 678 loop : -1.06 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 35 HIS 0.009 0.002 HIS I 355 PHE 0.017 0.002 PHE I 361 TYR 0.022 0.002 TYR K 50 ARG 0.006 0.001 ARG J 542 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 553) hydrogen bonds : angle 5.23736 ( 1476) SS BOND : bond 0.00501 ( 42) SS BOND : angle 1.50195 ( 84) covalent geometry : bond 0.00584 (19458) covalent geometry : angle 0.70531 (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 411 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 321 time to evaluate : 1.998 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 114 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7275 (mt0) REVERT: A 246 GLN cc_start: 0.7166 (mp10) cc_final: 0.6816 (tp-100) REVERT: A 396 MET cc_start: 0.8696 (pmm) cc_final: 0.7505 (mtt) REVERT: B 617 ARG cc_start: 0.8335 (mmt-90) cc_final: 0.5655 (ttp-170) REVERT: B 630 GLN cc_start: 0.8858 (mp10) cc_final: 0.8471 (mt0) REVERT: C 71 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8291 (pmt-80) REVERT: C 75 MET cc_start: 0.8258 (mtp) cc_final: 0.8010 (mtm) REVERT: E 67 ASN cc_start: 0.8081 (t0) cc_final: 0.7784 (t0) REVERT: E 114 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7073 (mt0) REVERT: E 198 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8795 (t) REVERT: E 396 MET cc_start: 0.8758 (pmm) cc_final: 0.7653 (mtt) REVERT: E 432 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7868 (ttm-80) REVERT: F 617 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.5607 (ttp-170) REVERT: G 39 GLN cc_start: 0.8219 (tt0) cc_final: 0.7871 (tt0) REVERT: G 71 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7917 (pmt-80) REVERT: I 82 GLN cc_start: 0.8032 (mm-40) cc_final: 0.6936 (pm20) REVERT: I 114 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7260 (mt0) REVERT: I 396 MET cc_start: 0.8772 (pmm) cc_final: 0.7589 (mtt) REVERT: I 458 TYR cc_start: 0.8172 (t80) cc_final: 0.7900 (t80) REVERT: J 540 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7364 (tm-30) REVERT: J 617 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.5555 (ttp-170) REVERT: J 630 GLN cc_start: 0.8770 (mp10) cc_final: 0.8526 (mt0) REVERT: K 39 GLN cc_start: 0.8297 (tt0) cc_final: 0.8056 (tt0) REVERT: K 75 MET cc_start: 0.8134 (mtp) cc_final: 0.7837 (mtp) REVERT: L 90 GLN cc_start: 0.9402 (pp30) cc_final: 0.9126 (pp30) outliers start: 90 outliers final: 62 residues processed: 376 average time/residue: 0.3026 time to fit residues: 172.4015 Evaluate side-chains 379 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 314 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 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 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 337 LYS 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 25 SER 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 C residue 71 ARG 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 198 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 ARG 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 11 VAL Chi-restraints excluded: chain G residue 17 THR 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 G residue 71 ARG Chi-restraints excluded: chain I residue 99 ASP 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 207 LYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 296 CYS 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 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 17 THR Chi-restraints excluded: chain K residue 45 PHE Chi-restraints excluded: chain K residue 51 ILE 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: 8.9990 chunk 113 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 23 optimal weight: 0.3980 chunk 129 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** ** G 6 GLN ** 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** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.158479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.138352 restraints weight = 23987.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.136547 restraints weight = 38229.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.130453 restraints weight = 40092.527| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19500 Z= 0.145 Angle : 0.636 12.842 26490 Z= 0.336 Chirality : 0.045 0.230 2937 Planarity : 0.004 0.052 3378 Dihedral : 5.477 25.381 2637 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 3.76 % Allowed : 18.43 % Favored : 77.81 % 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: -0.49 (0.17), residues: 2379 helix: 1.99 (0.28), residues: 363 sheet: -0.21 (0.20), residues: 648 loop : -1.05 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 35 HIS 0.009 0.002 HIS I 355 PHE 0.010 0.001 PHE J 522 TYR 0.019 0.002 TYR H 91 ARG 0.004 0.000 ARG J 542 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 553) hydrogen bonds : angle 5.09308 ( 1476) SS BOND : bond 0.00474 ( 42) SS BOND : angle 1.39298 ( 84) covalent geometry : bond 0.00335 (19458) covalent geometry : angle 0.63204 (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 404 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 325 time to evaluate : 1.964 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: 0.8275 (m100) cc_final: 0.7468 (m-10) REVERT: A 50 THR cc_start: 0.8760 (t) cc_final: 0.8553 (m) REVERT: A 51 THR cc_start: 0.8822 (m) cc_final: 0.8607 (p) REVERT: A 114 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7262 (mt0) REVERT: A 178 LYS cc_start: 0.8014 (mttp) cc_final: 0.7743 (mtmm) REVERT: A 246 GLN cc_start: 0.7174 (mp10) cc_final: 0.6675 (tp-100) REVERT: A 396 MET cc_start: 0.8610 (pmm) cc_final: 0.7225 (mtt) REVERT: A 434 MET cc_start: 0.8119 (ptm) cc_final: 0.7877 (ptp) REVERT: A 465 THR cc_start: 0.9393 (m) cc_final: 0.8853 (p) REVERT: B 617 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.5317 (ttp-170) REVERT: D 32 ASN cc_start: 0.8670 (m110) cc_final: 0.8324 (m-40) REVERT: E 50 THR cc_start: 0.8592 (t) cc_final: 0.8311 (m) REVERT: E 114 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7012 (mt0) REVERT: E 198 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8844 (t) REVERT: E 396 MET cc_start: 0.8813 (pmm) cc_final: 0.7455 (mtt) REVERT: F 537 LEU cc_start: 0.8601 (mt) cc_final: 0.8369 (mt) REVERT: F 617 ARG cc_start: 0.8333 (mmt-90) cc_final: 0.4303 (ttp-170) REVERT: F 628 TRP cc_start: 0.8105 (m100) cc_final: 0.7869 (m100) REVERT: G 39 GLN cc_start: 0.8358 (tt0) cc_final: 0.7947 (tt0) REVERT: G 71 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7971 (pmt-80) REVERT: I 35 TRP cc_start: 0.8235 (m100) cc_final: 0.7219 (m-10) REVERT: I 50 THR cc_start: 0.8601 (t) cc_final: 0.8379 (m) REVERT: I 72 HIS cc_start: 0.4246 (t70) cc_final: 0.4030 (t-90) REVERT: I 82 GLN cc_start: 0.8099 (mm-40) cc_final: 0.6744 (pm20) REVERT: I 114 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7258 (mt0) REVERT: I 396 MET cc_start: 0.8856 (pmm) cc_final: 0.7487 (mtt) REVERT: I 458 TYR cc_start: 0.8262 (t80) cc_final: 0.7954 (t80) REVERT: J 540 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7350 (tm-30) REVERT: J 617 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.5288 (ttp-170) REVERT: J 630 GLN cc_start: 0.8852 (mp10) cc_final: 0.8548 (mt0) REVERT: K 39 GLN cc_start: 0.8435 (tt0) cc_final: 0.8164 (tt0) REVERT: L 32 ASN cc_start: 0.8655 (m110) cc_final: 0.8355 (m110) REVERT: L 90 GLN cc_start: 0.9362 (pp30) cc_final: 0.9073 (pp30) outliers start: 79 outliers final: 56 residues processed: 376 average time/residue: 0.3068 time to fit residues: 176.3854 Evaluate side-chains 363 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 305 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 337 LYS 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 640 GLN Chi-restraints excluded: chain C residue 6 GLN 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 D residue 3 VAL 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 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 261 LEU 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 G residue 2 VAL 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 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 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 K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 45 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 69 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 204 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 32 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** 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** J 651 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.157439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.136670 restraints weight = 24011.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134635 restraints weight = 39801.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.128598 restraints weight = 42508.143| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19500 Z= 0.172 Angle : 0.656 12.646 26490 Z= 0.344 Chirality : 0.045 0.236 2937 Planarity : 0.004 0.059 3378 Dihedral : 5.448 25.434 2637 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 3.76 % Allowed : 18.81 % 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: -0.51 (0.17), residues: 2379 helix: 2.02 (0.28), residues: 363 sheet: -0.19 (0.21), residues: 648 loop : -1.09 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E 35 HIS 0.010 0.002 HIS I 355 PHE 0.011 0.001 PHE I 361 TYR 0.016 0.002 TYR G 50 ARG 0.004 0.000 ARG J 542 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 553) hydrogen bonds : angle 5.10147 ( 1476) SS BOND : bond 0.00483 ( 42) SS BOND : angle 1.38185 ( 84) covalent geometry : bond 0.00406 (19458) covalent geometry : angle 0.65213 (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 392 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 313 time to evaluate : 1.989 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 51 THR cc_start: 0.8853 (m) cc_final: 0.8608 (p) REVERT: A 114 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7204 (mt0) REVERT: A 246 GLN cc_start: 0.7112 (mp10) cc_final: 0.6734 (tp-100) REVERT: A 396 MET cc_start: 0.8564 (pmm) cc_final: 0.7423 (mtt) REVERT: A 434 MET cc_start: 0.8058 (ptm) cc_final: 0.7848 (ptp) REVERT: A 465 THR cc_start: 0.9380 (m) cc_final: 0.8880 (p) REVERT: B 617 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.4828 (ttp-170) REVERT: B 630 GLN cc_start: 0.8806 (mp10) cc_final: 0.8599 (mt0) REVERT: C 71 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8071 (pmt-80) REVERT: E 114 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7508 (mt0) REVERT: E 198 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8779 (t) REVERT: E 396 MET cc_start: 0.8783 (pmm) cc_final: 0.7665 (mtt) REVERT: F 537 LEU cc_start: 0.8630 (mt) cc_final: 0.8408 (mt) REVERT: F 617 ARG cc_start: 0.7392 (mmt-90) cc_final: 0.5177 (ttp-170) REVERT: G 39 GLN cc_start: 0.8303 (tt0) cc_final: 0.7897 (tt0) REVERT: G 71 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8017 (pmt-80) REVERT: I 35 TRP cc_start: 0.8249 (m100) cc_final: 0.7423 (m-10) REVERT: I 114 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7366 (mt0) REVERT: I 396 MET cc_start: 0.8804 (pmm) cc_final: 0.7643 (mtt) REVERT: I 458 TYR cc_start: 0.8199 (t80) cc_final: 0.7908 (t80) REVERT: J 540 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7330 (tm-30) REVERT: J 617 ARG cc_start: 0.8044 (mmt-90) cc_final: 0.5369 (ttp-170) REVERT: K 6 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: K 39 GLN cc_start: 0.8426 (tt0) cc_final: 0.8155 (tt0) REVERT: L 32 ASN cc_start: 0.8589 (m110) cc_final: 0.8376 (m-40) REVERT: L 90 GLN cc_start: 0.9400 (pp30) cc_final: 0.9144 (pp30) outliers start: 79 outliers final: 66 residues processed: 363 average time/residue: 0.3049 time to fit residues: 168.5503 Evaluate side-chains 376 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 306 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 430 VAL 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 B residue 640 GLN 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 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 3 VAL 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 D residue 75 ILE 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 198 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 213 ILE 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 G residue 2 VAL 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 17 GLU 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 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 651 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 45 PHE 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 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 169 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 651 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.157192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.136715 restraints weight = 24354.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.135245 restraints weight = 39318.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.128881 restraints weight = 40594.653| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19500 Z= 0.187 Angle : 0.663 12.749 26490 Z= 0.349 Chirality : 0.046 0.222 2937 Planarity : 0.004 0.053 3378 Dihedral : 5.463 25.711 2637 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 3.76 % Allowed : 19.14 % Favored : 77.10 % 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: -0.59 (0.17), residues: 2379 helix: 2.00 (0.28), residues: 363 sheet: -0.32 (0.20), residues: 678 loop : -1.12 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 35 HIS 0.010 0.002 HIS I 355 PHE 0.012 0.002 PHE I 361 TYR 0.018 0.002 TYR G 50 ARG 0.004 0.000 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 553) hydrogen bonds : angle 5.14336 ( 1476) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.34248 ( 84) covalent geometry : bond 0.00440 (19458) covalent geometry : angle 0.66021 (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 402 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 323 time to evaluate : 2.127 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 114 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7413 (mt0) REVERT: A 246 GLN cc_start: 0.7240 (mp10) cc_final: 0.6745 (tp-100) REVERT: A 396 MET cc_start: 0.8465 (pmm) cc_final: 0.7374 (mtt) REVERT: A 443 ILE cc_start: 0.8107 (tp) cc_final: 0.7856 (mm) REVERT: A 465 THR cc_start: 0.9393 (m) cc_final: 0.8862 (p) REVERT: B 617 ARG cc_start: 0.7731 (mmt-90) cc_final: 0.5045 (ttp-170) REVERT: C 64 ARG cc_start: 0.8962 (tpp80) cc_final: 0.8589 (ttm-80) REVERT: C 71 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8126 (pmt-80) REVERT: C 75 MET cc_start: 0.8244 (mtp) cc_final: 0.7966 (mtm) REVERT: E 35 TRP cc_start: 0.8163 (m-10) cc_final: 0.7923 (m-10) REVERT: E 114 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7448 (mt0) REVERT: E 198 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8781 (t) REVERT: E 396 MET cc_start: 0.8750 (pmm) cc_final: 0.7541 (mtt) REVERT: E 500 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7395 (ttpt) REVERT: F 537 LEU cc_start: 0.8659 (mt) cc_final: 0.8420 (mt) REVERT: F 617 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.5134 (ttp-170) REVERT: G 39 GLN cc_start: 0.8339 (tt0) cc_final: 0.7922 (tt0) REVERT: G 71 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7949 (pmt-80) REVERT: I 35 TRP cc_start: 0.8264 (m100) cc_final: 0.7332 (m-10) REVERT: I 114 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7313 (mt0) REVERT: I 396 MET cc_start: 0.8780 (pmm) cc_final: 0.7590 (mtt) REVERT: I 426 MET cc_start: 0.8335 (mtt) cc_final: 0.7590 (mmt) REVERT: I 458 TYR cc_start: 0.8311 (t80) cc_final: 0.7973 (t80) REVERT: J 540 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7324 (tm-30) REVERT: J 617 ARG cc_start: 0.8141 (mmt-90) cc_final: 0.5250 (ttp-170) REVERT: K 39 GLN cc_start: 0.8452 (tt0) cc_final: 0.8166 (tt0) REVERT: L 32 ASN cc_start: 0.8662 (m-40) cc_final: 0.8366 (m110) REVERT: L 90 GLN cc_start: 0.9421 (pp30) cc_final: 0.9111 (pp30) outliers start: 79 outliers final: 64 residues processed: 370 average time/residue: 0.3059 time to fit residues: 172.7469 Evaluate side-chains 380 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 430 VAL 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 B residue 640 GLN 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 3 VAL 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 200 VAL Chi-restraints excluded: chain E residue 207 LYS 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 642 ILE Chi-restraints excluded: chain G residue 2 VAL 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 17 GLU 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 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 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 2 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 45 PHE 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 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 223 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 164 optimal weight: 5.9990 chunk 88 optimal weight: 0.0020 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 0.0010 chunk 148 optimal weight: 0.9980 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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** ** G 6 GLN ** 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 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.160073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.140391 restraints weight = 23661.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.139205 restraints weight = 35526.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133112 restraints weight = 35749.439| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5058 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= 0.123 Angle : 0.632 12.632 26490 Z= 0.330 Chirality : 0.044 0.215 2937 Planarity : 0.004 0.051 3378 Dihedral : 5.307 26.575 2637 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 2.81 % Allowed : 20.33 % Favored : 76.86 % 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: -0.41 (0.17), residues: 2379 helix: 2.27 (0.29), residues: 363 sheet: -0.11 (0.21), residues: 648 loop : -1.08 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 35 HIS 0.010 0.001 HIS I 355 PHE 0.010 0.001 PHE J 522 TYR 0.022 0.002 TYR L 91 ARG 0.004 0.000 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 553) hydrogen bonds : angle 5.04806 ( 1476) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.21781 ( 84) covalent geometry : bond 0.00281 (19458) covalent geometry : angle 0.62958 (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 385 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7490 (mt0) REVERT: A 246 GLN cc_start: 0.7049 (mp10) cc_final: 0.6756 (tp-100) REVERT: A 396 MET cc_start: 0.8487 (pmm) cc_final: 0.7550 (mtt) REVERT: A 465 THR cc_start: 0.9331 (m) cc_final: 0.8838 (p) REVERT: B 617 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.5393 (ttp-170) REVERT: C 64 ARG cc_start: 0.8903 (tpp80) cc_final: 0.8539 (ttm-80) REVERT: E 35 TRP cc_start: 0.8088 (m-10) cc_final: 0.7794 (m-10) REVERT: E 45 TRP cc_start: 0.7748 (p90) cc_final: 0.7494 (p90) REVERT: E 396 MET cc_start: 0.8649 (pmm) cc_final: 0.7621 (mtt) REVERT: E 500 LYS cc_start: 0.7605 (ttpt) cc_final: 0.7362 (ttpt) REVERT: F 537 LEU cc_start: 0.8560 (mt) cc_final: 0.8338 (mt) REVERT: F 617 ARG cc_start: 0.8123 (mmt-90) cc_final: 0.5258 (ttp-170) REVERT: G 39 GLN cc_start: 0.8228 (tt0) cc_final: 0.7834 (tt0) REVERT: I 114 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7449 (mt0) REVERT: I 396 MET cc_start: 0.8685 (pmm) cc_final: 0.7737 (mtt) REVERT: I 426 MET cc_start: 0.8427 (mtt) cc_final: 0.8144 (mtt) REVERT: I 458 TYR cc_start: 0.8211 (t80) cc_final: 0.7909 (t80) REVERT: J 617 ARG cc_start: 0.8039 (mmt-90) cc_final: 0.5576 (ttp-170) REVERT: K 39 GLN cc_start: 0.8368 (tt0) cc_final: 0.8081 (tt0) REVERT: K 54 ASN cc_start: 0.9025 (p0) cc_final: 0.8756 (p0) REVERT: L 90 GLN cc_start: 0.9340 (pp30) cc_final: 0.9118 (pp30) outliers start: 59 outliers final: 53 residues processed: 363 average time/residue: 0.3124 time to fit residues: 172.3274 Evaluate side-chains 360 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 2.234 ------------------------------------------------------------------------------- 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 296 CYS 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 640 GLN 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 D residue 3 VAL 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 196 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 213 ILE 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 G residue 11 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 59 TYR 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 200 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 11 VAL Chi-restraints excluded: chain K residue 45 PHE 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: 20.0000 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 101 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN B 607 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** 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 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.157747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.132497 restraints weight = 24176.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.131151 restraints weight = 37675.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.131392 restraints weight = 37375.506| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19500 Z= 0.191 Angle : 0.668 12.689 26490 Z= 0.350 Chirality : 0.046 0.217 2937 Planarity : 0.004 0.053 3378 Dihedral : 5.363 26.725 2637 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 3.00 % Allowed : 20.57 % Favored : 76.43 % 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: -0.52 (0.17), residues: 2379 helix: 2.13 (0.28), residues: 363 sheet: -0.27 (0.20), residues: 678 loop : -1.11 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 35 HIS 0.011 0.002 HIS I 355 PHE 0.012 0.002 PHE I 361 TYR 0.029 0.002 TYR L 91 ARG 0.004 0.000 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 553) hydrogen bonds : angle 5.11149 ( 1476) SS BOND : bond 0.00509 ( 42) SS BOND : angle 1.58049 ( 84) covalent geometry : bond 0.00452 (19458) covalent geometry : angle 0.66261 (26406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5669.31 seconds wall clock time: 100 minutes 20.44 seconds (6020.44 seconds total)