Starting phenix.real_space_refine on Tue Nov 19 07:00:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxj_40854/11_2024/8sxj_40854_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxj_40854/11_2024/8sxj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxj_40854/11_2024/8sxj_40854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxj_40854/11_2024/8sxj_40854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxj_40854/11_2024/8sxj_40854_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxj_40854/11_2024/8sxj_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 11.46, 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: 4.51 Conformation dependent library (CDL) restraints added in 2.4 seconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 37 sheets defined 19.5% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.600A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.614A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.668A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.536A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.682A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.543A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 100 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 353 removed outlier: 4.525A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.503A pdb=" N PHE E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 482 removed outlier: 3.674A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.532A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 546 No H-bonds generated for 'chain 'F' and resid 544 through 546' Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.678A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 100 through 117 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 334 through 353 removed outlier: 4.537A pdb=" N GLU I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 392 removed outlier: 3.508A pdb=" N PHE I 391 " --> pdb=" O THR I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 482 removed outlier: 3.666A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU I 480 " --> pdb=" O ASN I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 543 removed outlier: 3.527A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 544 through 546 No H-bonds generated for 'chain 'J' and resid 544 through 546' Processing helix chain 'J' and resid 572 through 596 removed outlier: 3.678A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) Processing helix chain 'J' and resid 621 through 625 Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 664 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 5.220A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.637A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.434A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 304 removed outlier: 4.275A pdb=" N GLN A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 320 through 323 current: chain 'A' and resid 382 through 385 removed outlier: 3.967A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 414 through 421 current: chain 'A' and resid 466 through 468 Processing sheet with id=AA8, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 361 removed outlier: 3.898A pdb=" N ARG A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 removed outlier: 4.170A pdb=" N SER C 21 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100B through 103 Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 54 current: chain 'D' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'E' and resid 493 through 497 removed outlier: 5.217A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.639A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.372A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.761A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 382 through 385 removed outlier: 3.901A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 414 through 421 current: chain 'E' and resid 466 through 468 Processing sheet with id=AC3, first strand: chain 'E' and resid 358 through 361 removed outlier: 3.887A pdb=" N ARG E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.171A pdb=" N SER G 21 " --> pdb=" O TYR G 7 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100B through 103 Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 53 through 54 current: chain 'H' and resid 97 through 98 Processing sheet with id=AC8, first strand: chain 'I' and resid 493 through 497 removed outlier: 5.223A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.640A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD2, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'I' and resid 170 through 177 Processing sheet with id=AD4, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.045A pdb=" N VAL I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR I 435 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 308 removed outlier: 4.034A pdb=" N GLN I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR I 320 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 316 through 323 current: chain 'I' and resid 382 through 385 removed outlier: 3.900A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 414 through 421 current: chain 'I' and resid 466 through 468 Processing sheet with id=AD6, first strand: chain 'I' and resid 358 through 361 removed outlier: 3.893A pdb=" N ARG I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 7 removed outlier: 4.146A pdb=" N SER K 21 " --> pdb=" O TYR K 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR K 77 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100B through 103 Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 553 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 5.17 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 43.400 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.440 ------------------------------------------------------------------------------- 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 19458 Z= 0.946 Angle : 1.763 25.222 26406 Z= 1.167 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 *********************** 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 : 2.126 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: 0.3757 time to fit residues: 307.8417 Evaluate side-chains 349 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 339 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 19458 Z= 0.217 Angle : 0.756 12.825 26406 Z= 0.403 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 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 354 time to evaluate : 2.077 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: 0.8225 (m100) cc_final: 0.7976 (m100) REVERT: A 178 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8233 (tmtt) REVERT: A 396 MET cc_start: 0.9011 (pmm) cc_final: 0.7260 (mtt) REVERT: C 75 MET cc_start: 0.7755 (mmm) cc_final: 0.7374 (mtp) REVERT: E 178 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8212 (tmtt) REVERT: E 275 GLU cc_start: 0.7845 (tp30) cc_final: 0.7494 (tp30) REVERT: E 396 MET cc_start: 0.8880 (pmm) cc_final: 0.7371 (mtt) REVERT: E 426 MET cc_start: 0.8008 (mtt) cc_final: 0.7532 (mmt) REVERT: G 39 GLN cc_start: 0.7918 (tt0) cc_final: 0.7659 (tt0) REVERT: H 100 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8225 (mm-40) REVERT: I 35 TRP cc_start: 0.8224 (m100) cc_final: 0.7752 (m-10) REVERT: I 95 MET cc_start: 0.7613 (ptm) cc_final: 0.7403 (ptm) REVERT: I 308 ARG cc_start: 0.7603 (mtp85) cc_final: 0.6885 (mmp-170) REVERT: I 396 MET cc_start: 0.8788 (pmm) cc_final: 0.7295 (mtt) REVERT: I 434 MET cc_start: 0.7671 (ttp) cc_final: 0.7455 (ttp) REVERT: K 75 MET cc_start: 0.7691 (mmm) cc_final: 0.7421 (mtp) outliers start: 61 outliers final: 30 residues processed: 393 average time/residue: 0.3237 time to fit residues: 191.9821 Evaluate side-chains 321 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 2.105 ------------------------------------------------------------------------------- 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 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 119 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 179 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 73 optimal weight: 0.0060 chunk 172 optimal weight: 0.0870 overall best weight: 0.4574 ------------------------------------------------------------------------------- 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** B 607 ASN E 72 HIS E 300 ASN I 72 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19458 Z= 0.174 Angle : 0.664 12.472 26406 Z= 0.354 Chirality : 0.045 0.208 2937 Planarity : 0.004 0.043 3378 Dihedral : 6.086 32.082 2640 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.04 % Favored : 94.70 % Rotamer: Outliers : 2.29 % Allowed : 14.52 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2379 helix: 2.10 (0.28), residues: 363 sheet: -0.35 (0.19), residues: 654 loop : -0.85 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 35 HIS 0.009 0.001 HIS E 249 PHE 0.012 0.001 PHE I 176 TYR 0.028 0.002 TYR E 482 ARG 0.008 0.001 ARG H 45 *********************** 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 390 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 342 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8196 (m100) cc_final: 0.7910 (m100) REVERT: A 95 MET cc_start: 0.7611 (ptm) cc_final: 0.7290 (ptm) REVERT: A 178 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8142 (tmtt) REVERT: A 396 MET cc_start: 0.8921 (pmm) cc_final: 0.7304 (mtt) REVERT: A 498 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6474 (tpt-90) REVERT: B 617 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.5741 (ttp-170) REVERT: C 46 GLU cc_start: 0.7359 (tt0) cc_final: 0.7097 (mt-10) REVERT: C 75 MET cc_start: 0.7769 (mmm) cc_final: 0.7426 (mtp) REVERT: E 178 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8133 (tmtt) REVERT: E 275 GLU cc_start: 0.7764 (tp30) cc_final: 0.7285 (tp30) REVERT: E 396 MET cc_start: 0.8852 (pmm) cc_final: 0.7403 (mtt) REVERT: E 426 MET cc_start: 0.7917 (mtt) cc_final: 0.7647 (mmt) REVERT: F 634 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7986 (mt-10) REVERT: G 39 GLN cc_start: 0.8058 (tt0) cc_final: 0.7831 (tt0) REVERT: G 75 MET cc_start: 0.7554 (mmm) cc_final: 0.7232 (mtp) REVERT: I 35 TRP cc_start: 0.8114 (m100) cc_final: 0.7631 (m-10) REVERT: I 308 ARG cc_start: 0.7498 (mtp85) cc_final: 0.6826 (mmp-170) REVERT: I 396 MET cc_start: 0.8763 (pmm) cc_final: 0.7543 (mtt) REVERT: J 530 MET cc_start: 0.6905 (mmt) cc_final: 0.6520 (mmm) REVERT: J 634 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7969 (mt-10) REVERT: J 635 ILE cc_start: 0.8429 (mm) cc_final: 0.8131 (mm) REVERT: K 6 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: K 46 GLU cc_start: 0.7228 (tt0) cc_final: 0.6988 (mt-10) outliers start: 48 outliers final: 30 residues processed: 376 average time/residue: 0.3232 time to fit residues: 184.6804 Evaluate side-chains 327 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 215 ILE 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 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 198 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 246 GLN B 658 GLN E 72 HIS E 246 GLN F 651 ASN I 72 HIS I 105 HIS I 246 GLN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN J 658 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19458 Z= 0.340 Angle : 0.707 12.715 26406 Z= 0.375 Chirality : 0.047 0.222 2937 Planarity : 0.005 0.060 3378 Dihedral : 5.924 30.658 2639 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.38 % Favored : 94.37 % Rotamer: Outliers : 4.05 % Allowed : 15.76 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2379 helix: 1.54 (0.28), residues: 381 sheet: -0.44 (0.19), residues: 693 loop : -0.93 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 35 HIS 0.008 0.002 HIS I 249 PHE 0.016 0.002 PHE I 361 TYR 0.020 0.002 TYR E 482 ARG 0.005 0.001 ARG C 71 *********************** 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 427 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 342 time to evaluate : 2.042 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: 0.8270 (m100) cc_final: 0.7987 (m-10) REVERT: A 49 LYS cc_start: 0.8455 (mptt) cc_final: 0.8176 (ptmm) REVERT: A 178 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8151 (mtmm) REVERT: A 246 GLN cc_start: 0.6873 (mp10) cc_final: 0.6478 (mm-40) REVERT: A 396 MET cc_start: 0.8829 (pmm) cc_final: 0.7315 (mtt) REVERT: A 426 MET cc_start: 0.8372 (mmm) cc_final: 0.7830 (mmt) REVERT: B 617 ARG cc_start: 0.8127 (mmt-90) cc_final: 0.5680 (ttp-170) REVERT: C 75 MET cc_start: 0.7820 (mmm) cc_final: 0.7520 (mtp) REVERT: E 49 LYS cc_start: 0.8406 (mptt) cc_final: 0.8126 (mttp) REVERT: E 67 ASN cc_start: 0.8075 (t0) cc_final: 0.7533 (t0) REVERT: E 178 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8074 (tmtt) REVERT: E 180 ASP cc_start: 0.8564 (m-30) cc_final: 0.8337 (t0) REVERT: E 396 MET cc_start: 0.8859 (pmm) cc_final: 0.7457 (mtt) REVERT: E 426 MET cc_start: 0.8217 (mtt) cc_final: 0.7612 (mmt) REVERT: E 458 TYR cc_start: 0.8313 (t80) cc_final: 0.7909 (t80) REVERT: F 617 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.5457 (ttp-170) REVERT: F 628 TRP cc_start: 0.8128 (m100) cc_final: 0.7775 (m100) REVERT: G 39 GLN cc_start: 0.8169 (tt0) cc_final: 0.7950 (tt0) REVERT: G 75 MET cc_start: 0.7679 (mmm) cc_final: 0.7305 (mtp) REVERT: I 290 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7879 (tm-30) REVERT: I 308 ARG cc_start: 0.7755 (mtp85) cc_final: 0.6979 (mmp-170) REVERT: I 396 MET cc_start: 0.8800 (pmm) cc_final: 0.7607 (mtt) REVERT: J 540 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7119 (tm-30) REVERT: J 617 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.5480 (ttp-170) REVERT: K 39 GLN cc_start: 0.8140 (tt0) cc_final: 0.7890 (tt0) outliers start: 85 outliers final: 55 residues processed: 391 average time/residue: 0.3442 time to fit residues: 202.7833 Evaluate side-chains 363 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 2.271 ------------------------------------------------------------------------------- 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 278 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 THR 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 641 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE 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 281 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain F residue 528 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 H residue 37 GLN 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 281 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 626 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 425 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS I 195 ASN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19458 Z= 0.356 Angle : 0.694 12.706 26406 Z= 0.370 Chirality : 0.047 0.218 2937 Planarity : 0.004 0.051 3378 Dihedral : 5.858 28.341 2639 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.25 % Favored : 94.54 % Rotamer: Outliers : 3.86 % Allowed : 17.19 % Favored : 78.95 % 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: -0.64 (0.17), residues: 2379 helix: 1.65 (0.28), residues: 360 sheet: -0.48 (0.19), residues: 729 loop : -0.98 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 35 HIS 0.008 0.002 HIS I 355 PHE 0.016 0.002 PHE I 361 TYR 0.021 0.002 TYR K 50 ARG 0.007 0.001 ARG B 542 *********************** 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 423 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 342 time to evaluate : 2.258 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: A 35 TRP cc_start: 0.8263 (m100) cc_final: 0.7844 (m-10) REVERT: A 49 LYS cc_start: 0.8472 (mptt) cc_final: 0.8243 (ptmm) REVERT: A 178 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8167 (mtmm) REVERT: A 246 GLN cc_start: 0.7029 (mp10) cc_final: 0.6674 (tp-100) REVERT: A 396 MET cc_start: 0.8773 (pmm) cc_final: 0.7356 (mtt) REVERT: A 426 MET cc_start: 0.8412 (mmm) cc_final: 0.8195 (mmt) REVERT: B 617 ARG cc_start: 0.8247 (mmt-90) cc_final: 0.5590 (ttp-170) REVERT: B 628 TRP cc_start: 0.8007 (m100) cc_final: 0.7748 (m100) REVERT: C 75 MET cc_start: 0.7939 (mmm) cc_final: 0.7559 (mtp) REVERT: D 90 GLN cc_start: 0.9361 (pp30) cc_final: 0.9051 (pp30) REVERT: E 49 LYS cc_start: 0.8427 (mptt) cc_final: 0.7899 (mttp) REVERT: E 50 THR cc_start: 0.8522 (t) cc_final: 0.8277 (m) REVERT: E 114 GLN cc_start: 0.7700 (mm-40) cc_final: 0.6998 (mt0) REVERT: E 178 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7925 (tmtt) REVERT: E 180 ASP cc_start: 0.8632 (m-30) cc_final: 0.8285 (t0) REVERT: E 246 GLN cc_start: 0.6914 (mp10) cc_final: 0.6687 (tp-100) REVERT: E 396 MET cc_start: 0.8835 (pmm) cc_final: 0.7515 (mtt) REVERT: E 458 TYR cc_start: 0.8392 (t80) cc_final: 0.7968 (t80) REVERT: F 617 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.5429 (ttp-170) REVERT: G 39 GLN cc_start: 0.8221 (tt0) cc_final: 0.7982 (tt0) REVERT: G 46 GLU cc_start: 0.7550 (tt0) cc_final: 0.7336 (mt-10) REVERT: G 75 MET cc_start: 0.7724 (mmm) cc_final: 0.7371 (mtp) REVERT: H 90 GLN cc_start: 0.9351 (pp30) cc_final: 0.8888 (pp30) REVERT: I 50 THR cc_start: 0.8664 (t) cc_final: 0.8376 (m) REVERT: I 72 HIS cc_start: 0.4301 (t70) cc_final: 0.4084 (t-90) REVERT: I 114 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7078 (mt0) REVERT: I 396 MET cc_start: 0.8796 (pmm) cc_final: 0.7583 (mtt) REVERT: I 458 TYR cc_start: 0.8308 (t80) cc_final: 0.8103 (t80) REVERT: J 540 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7232 (tm-30) REVERT: J 617 ARG cc_start: 0.7933 (mmt-90) cc_final: 0.5508 (ttp-170) REVERT: K 20 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7229 (mp) REVERT: K 39 GLN cc_start: 0.8205 (tt0) cc_final: 0.7973 (tt0) REVERT: L 90 GLN cc_start: 0.9340 (pp30) cc_final: 0.8882 (pp30) outliers start: 81 outliers final: 61 residues processed: 384 average time/residue: 0.3176 time to fit residues: 186.0957 Evaluate side-chains 382 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 320 time to evaluate : 2.236 ------------------------------------------------------------------------------- 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 195 ASN 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 281 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 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 132 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 434 MET 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 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 59 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 36 VAL 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 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain J residue 608 VAL 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 20 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 229 optimal weight: 0.0370 chunk 190 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- 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 625 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN I 195 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19458 Z= 0.229 Angle : 0.635 12.676 26406 Z= 0.337 Chirality : 0.045 0.208 2937 Planarity : 0.004 0.051 3378 Dihedral : 5.634 26.128 2639 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 3.95 % Allowed : 17.71 % Favored : 78.33 % 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: -0.50 (0.17), residues: 2379 helix: 1.89 (0.28), residues: 363 sheet: -0.36 (0.19), residues: 693 loop : -0.94 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 35 HIS 0.009 0.002 HIS I 355 PHE 0.011 0.001 PHE E 361 TYR 0.023 0.002 TYR K 7 ARG 0.006 0.000 ARG B 542 *********************** 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 413 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 330 time to evaluate : 2.261 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: 0.8221 (m100) cc_final: 0.7804 (m-10) REVERT: A 49 LYS cc_start: 0.8491 (mptt) cc_final: 0.8237 (ptmm) REVERT: A 114 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7039 (mt0) REVERT: A 178 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8129 (mtmm) REVERT: A 246 GLN cc_start: 0.7002 (mp10) cc_final: 0.6645 (tp-100) REVERT: A 396 MET cc_start: 0.8676 (pmm) cc_final: 0.7364 (mtt) REVERT: B 617 ARG cc_start: 0.8239 (mmt-90) cc_final: 0.5621 (ttp-170) REVERT: C 75 MET cc_start: 0.7918 (mmm) cc_final: 0.7591 (mtp) REVERT: E 49 LYS cc_start: 0.8339 (mptt) cc_final: 0.7907 (ptmm) REVERT: E 50 THR cc_start: 0.8566 (t) cc_final: 0.8356 (m) REVERT: E 114 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7040 (mt0) REVERT: E 178 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7784 (tmtt) REVERT: E 198 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8749 (t) REVERT: E 275 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7667 (tp30) REVERT: E 396 MET cc_start: 0.8847 (pmm) cc_final: 0.7589 (mtt) REVERT: E 426 MET cc_start: 0.7879 (mtt) cc_final: 0.7394 (mmt) REVERT: E 458 TYR cc_start: 0.8423 (t80) cc_final: 0.7981 (t80) REVERT: F 617 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.5415 (ttp-170) REVERT: G 6 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: G 39 GLN cc_start: 0.8227 (tt0) cc_final: 0.7984 (tt0) REVERT: H 90 GLN cc_start: 0.9336 (pp30) cc_final: 0.8902 (pp30) REVERT: I 50 THR cc_start: 0.8614 (t) cc_final: 0.8320 (m) REVERT: I 114 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7200 (mt0) REVERT: I 396 MET cc_start: 0.8770 (pmm) cc_final: 0.7555 (mtt) REVERT: I 458 TYR cc_start: 0.8360 (t80) cc_final: 0.8132 (t80) REVERT: J 540 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7300 (tm-30) REVERT: J 617 ARG cc_start: 0.7929 (mmt-90) cc_final: 0.5520 (ttp-170) REVERT: K 39 GLN cc_start: 0.8223 (tt0) cc_final: 0.7972 (tt0) REVERT: L 90 GLN cc_start: 0.9317 (pp30) cc_final: 0.8947 (pp30) outliers start: 83 outliers final: 60 residues processed: 377 average time/residue: 0.3159 time to fit residues: 182.3815 Evaluate side-chains 370 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 2.088 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR 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 278 THR Chi-restraints excluded: chain A residue 281 VAL 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 C residue 6 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 125 LEU 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 359 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 167 optimal weight: 0.0170 chunk 129 optimal weight: 0.4980 chunk 193 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 228 optimal weight: 0.0050 chunk 142 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19458 Z= 0.152 Angle : 0.599 12.238 26406 Z= 0.317 Chirality : 0.043 0.212 2937 Planarity : 0.004 0.061 3378 Dihedral : 5.301 26.615 2637 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.25 % Rotamer: Outliers : 2.95 % Allowed : 18.24 % 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: -0.29 (0.17), residues: 2379 helix: 2.26 (0.28), residues: 363 sheet: -0.13 (0.20), residues: 663 loop : -0.92 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 35 HIS 0.008 0.001 HIS I 355 PHE 0.009 0.001 PHE E 176 TYR 0.019 0.001 TYR L 36 ARG 0.005 0.000 ARG F 542 *********************** 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 393 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 331 time to evaluate : 2.105 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: 0.8185 (m100) cc_final: 0.7797 (m-10) REVERT: A 50 THR cc_start: 0.8492 (t) cc_final: 0.8271 (m) REVERT: A 51 THR cc_start: 0.8603 (m) cc_final: 0.8387 (p) REVERT: A 114 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7175 (mt0) REVERT: A 178 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8109 (mtmm) REVERT: A 246 GLN cc_start: 0.6882 (mp10) cc_final: 0.6618 (tp-100) REVERT: A 396 MET cc_start: 0.8658 (pmm) cc_final: 0.7399 (mtt) REVERT: B 617 ARG cc_start: 0.8221 (mmt-90) cc_final: 0.5622 (ttp-170) REVERT: C 75 MET cc_start: 0.7858 (mmm) cc_final: 0.7561 (mtp) REVERT: E 35 TRP cc_start: 0.8194 (m-10) cc_final: 0.7971 (m-10) REVERT: E 50 THR cc_start: 0.8405 (t) cc_final: 0.8156 (m) REVERT: E 67 ASN cc_start: 0.7723 (t0) cc_final: 0.7409 (t0) REVERT: E 114 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7016 (mt0) REVERT: E 178 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7612 (tmtt) REVERT: E 198 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8733 (t) REVERT: E 396 MET cc_start: 0.8755 (pmm) cc_final: 0.7556 (mtt) REVERT: E 426 MET cc_start: 0.7776 (mtt) cc_final: 0.7572 (mmt) REVERT: E 458 TYR cc_start: 0.8412 (t80) cc_final: 0.7970 (t80) REVERT: F 537 LEU cc_start: 0.8556 (mt) cc_final: 0.8339 (mt) REVERT: F 617 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.5262 (ttp80) REVERT: G 39 GLN cc_start: 0.8243 (tt0) cc_final: 0.7882 (tt0) REVERT: H 90 GLN cc_start: 0.9277 (pp30) cc_final: 0.8902 (pp30) REVERT: I 35 TRP cc_start: 0.8128 (m100) cc_final: 0.7470 (m-10) REVERT: I 50 THR cc_start: 0.8572 (t) cc_final: 0.8269 (m) REVERT: I 114 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7310 (mt0) REVERT: I 308 ARG cc_start: 0.7659 (mtp85) cc_final: 0.6897 (mmp-170) REVERT: I 396 MET cc_start: 0.8738 (pmm) cc_final: 0.7573 (mtt) REVERT: J 617 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.5516 (ttp-170) REVERT: J 635 ILE cc_start: 0.8300 (mm) cc_final: 0.8027 (mm) REVERT: K 39 GLN cc_start: 0.8200 (tt0) cc_final: 0.7976 (tt0) outliers start: 62 outliers final: 46 residues processed: 367 average time/residue: 0.3122 time to fit residues: 175.9789 Evaluate side-chains 358 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 311 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE 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 127 CYS Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 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 51 ILE Chi-restraints excluded: chain K residue 80 MET 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 141 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN I 72 HIS I 216 HIS ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19458 Z= 0.269 Angle : 0.640 12.419 26406 Z= 0.335 Chirality : 0.045 0.211 2937 Planarity : 0.004 0.056 3378 Dihedral : 5.311 26.616 2637 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 2.81 % Allowed : 19.24 % Favored : 77.95 % 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: -0.39 (0.17), residues: 2379 helix: 2.13 (0.28), residues: 363 sheet: -0.24 (0.20), residues: 678 loop : -0.95 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 35 HIS 0.009 0.002 HIS I 355 PHE 0.012 0.002 PHE E 361 TYR 0.015 0.002 TYR K 50 ARG 0.005 0.000 ARG B 542 *********************** 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 375 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 316 time to evaluate : 2.107 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 49 LYS cc_start: 0.8355 (mptt) cc_final: 0.7897 (ptmm) REVERT: A 51 THR cc_start: 0.8669 (m) cc_final: 0.8465 (p) REVERT: A 114 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7165 (mt0) REVERT: A 178 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8049 (mtmm) REVERT: A 246 GLN cc_start: 0.7035 (mp10) cc_final: 0.6727 (tp-100) REVERT: A 396 MET cc_start: 0.8652 (pmm) cc_final: 0.7416 (mtt) REVERT: B 617 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.5641 (ttp-170) REVERT: C 75 MET cc_start: 0.7852 (mmm) cc_final: 0.7587 (mtp) REVERT: E 67 ASN cc_start: 0.7816 (t0) cc_final: 0.7584 (t0) REVERT: E 114 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7063 (mt0) REVERT: E 178 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7593 (tmtt) REVERT: E 198 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8753 (t) REVERT: E 396 MET cc_start: 0.8754 (pmm) cc_final: 0.7584 (mtt) REVERT: E 426 MET cc_start: 0.7922 (mtt) cc_final: 0.7501 (mmt) REVERT: F 617 ARG cc_start: 0.8151 (mmt-90) cc_final: 0.4663 (ttp-170) REVERT: G 6 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: G 39 GLN cc_start: 0.8277 (tt0) cc_final: 0.7891 (tt0) REVERT: H 90 GLN cc_start: 0.9344 (pp30) cc_final: 0.8870 (pp30) REVERT: I 35 TRP cc_start: 0.8179 (m100) cc_final: 0.7522 (m-10) REVERT: I 50 THR cc_start: 0.8589 (t) cc_final: 0.8292 (m) REVERT: I 114 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7289 (mt0) REVERT: I 396 MET cc_start: 0.8744 (pmm) cc_final: 0.7529 (mtt) REVERT: I 426 MET cc_start: 0.7807 (mtt) cc_final: 0.7489 (mmt) REVERT: I 458 TYR cc_start: 0.8365 (t80) cc_final: 0.8048 (t80) REVERT: J 540 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7201 (tm-30) REVERT: J 617 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.4835 (ttp-170) REVERT: K 39 GLN cc_start: 0.8240 (tt0) cc_final: 0.7972 (tt0) REVERT: L 90 GLN cc_start: 0.9336 (pp30) cc_final: 0.8843 (pp30) outliers start: 59 outliers final: 50 residues processed: 353 average time/residue: 0.3109 time to fit residues: 167.5028 Evaluate side-chains 358 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 306 time to evaluate : 2.058 ------------------------------------------------------------------------------- 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 195 ASN 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 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 85 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 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 96 VAL 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 109 ILE 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 213 ILE Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 467 ARG Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 0.6980 chunk 199 optimal weight: 0.1980 chunk 212 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN E 216 HIS ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19458 Z= 0.166 Angle : 0.605 12.449 26406 Z= 0.315 Chirality : 0.043 0.254 2937 Planarity : 0.004 0.050 3378 Dihedral : 5.131 26.989 2637 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 2.90 % Allowed : 19.10 % Favored : 78.00 % 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: -0.27 (0.17), residues: 2379 helix: 2.34 (0.29), residues: 363 sheet: -0.13 (0.20), residues: 678 loop : -0.93 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 35 HIS 0.009 0.001 HIS I 355 PHE 0.010 0.001 PHE H 62 TYR 0.013 0.001 TYR H 91 ARG 0.005 0.000 ARG C 64 *********************** 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 383 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 1.681 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: 0.8239 (m100) cc_final: 0.7735 (m-10) REVERT: A 178 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7897 (mtmm) REVERT: A 180 ASP cc_start: 0.8629 (t0) cc_final: 0.8221 (t0) REVERT: A 396 MET cc_start: 0.8558 (pmm) cc_final: 0.7415 (mtt) REVERT: A 434 MET cc_start: 0.7547 (ptp) cc_final: 0.6978 (ptp) REVERT: B 617 ARG cc_start: 0.8233 (mmt-90) cc_final: 0.5621 (ttp-170) REVERT: E 67 ASN cc_start: 0.7805 (t0) cc_final: 0.7591 (t0) REVERT: E 178 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7399 (tmtt) REVERT: E 198 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8778 (t) REVERT: E 396 MET cc_start: 0.8713 (pmm) cc_final: 0.7618 (mtt) REVERT: E 426 MET cc_start: 0.7747 (mtt) cc_final: 0.7515 (mmt) REVERT: F 537 LEU cc_start: 0.8572 (mt) cc_final: 0.8350 (mt) REVERT: F 617 ARG cc_start: 0.7420 (mmt-90) cc_final: 0.4989 (ttp-170) REVERT: F 628 TRP cc_start: 0.7876 (m100) cc_final: 0.7660 (m100) REVERT: G 6 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: G 39 GLN cc_start: 0.8268 (tt0) cc_final: 0.7878 (tt0) REVERT: G 75 MET cc_start: 0.7875 (mmm) cc_final: 0.7508 (mtp) REVERT: H 90 GLN cc_start: 0.9306 (pp30) cc_final: 0.8921 (pp30) REVERT: I 35 TRP cc_start: 0.8144 (m100) cc_final: 0.7530 (m-10) REVERT: I 50 THR cc_start: 0.8498 (t) cc_final: 0.8202 (m) REVERT: I 396 MET cc_start: 0.8711 (pmm) cc_final: 0.7671 (mtt) REVERT: I 426 MET cc_start: 0.7658 (mtt) cc_final: 0.7440 (mmt) REVERT: I 458 TYR cc_start: 0.8358 (t80) cc_final: 0.8058 (t80) REVERT: J 617 ARG cc_start: 0.7358 (mmt-90) cc_final: 0.5236 (ttp-170) REVERT: J 635 ILE cc_start: 0.8310 (mm) cc_final: 0.7945 (mm) REVERT: K 6 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: K 39 GLN cc_start: 0.8190 (tt0) cc_final: 0.7925 (tt0) REVERT: L 90 GLN cc_start: 0.9283 (pp30) cc_final: 0.8836 (pp30) outliers start: 61 outliers final: 48 residues processed: 358 average time/residue: 0.3289 time to fit residues: 179.6672 Evaluate side-chains 359 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 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 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 85 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 181 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 96 VAL 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 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 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 145 optimal weight: 0.1980 chunk 115 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19458 Z= 0.196 Angle : 0.613 12.408 26406 Z= 0.321 Chirality : 0.044 0.250 2937 Planarity : 0.004 0.051 3378 Dihedral : 5.131 27.218 2637 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 2.57 % Allowed : 19.62 % 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: -0.27 (0.17), residues: 2379 helix: 2.37 (0.28), residues: 363 sheet: -0.12 (0.20), residues: 678 loop : -0.94 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP E 35 HIS 0.010 0.002 HIS I 355 PHE 0.009 0.001 PHE J 522 TYR 0.013 0.002 TYR C 7 ARG 0.007 0.000 ARG E 273 ********************** 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 368 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 314 time to evaluate : 2.114 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 178 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7781 (ttpp) REVERT: A 180 ASP cc_start: 0.8701 (t0) cc_final: 0.8287 (t0) REVERT: A 246 GLN cc_start: 0.6990 (mp10) cc_final: 0.6719 (tp-100) REVERT: A 396 MET cc_start: 0.8513 (pmm) cc_final: 0.7420 (mtt) REVERT: A 465 THR cc_start: 0.9325 (m) cc_final: 0.8781 (p) REVERT: B 617 ARG cc_start: 0.8271 (mmt-90) cc_final: 0.5689 (ttp-170) REVERT: E 67 ASN cc_start: 0.7788 (t0) cc_final: 0.7558 (t0) REVERT: E 178 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7416 (tmtt) REVERT: E 198 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8729 (t) REVERT: E 308 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7259 (mmt180) REVERT: E 396 MET cc_start: 0.8699 (pmm) cc_final: 0.7671 (mtt) REVERT: E 426 MET cc_start: 0.7778 (mtt) cc_final: 0.7523 (mmt) REVERT: F 537 LEU cc_start: 0.8599 (mt) cc_final: 0.8383 (mt) REVERT: F 617 ARG cc_start: 0.7514 (mmt-90) cc_final: 0.4959 (ttp-170) REVERT: G 39 GLN cc_start: 0.8280 (tt0) cc_final: 0.7889 (tt0) REVERT: G 75 MET cc_start: 0.7809 (mmm) cc_final: 0.7510 (mtp) REVERT: H 90 GLN cc_start: 0.9312 (pp30) cc_final: 0.8878 (pp30) REVERT: I 35 TRP cc_start: 0.8153 (m100) cc_final: 0.7561 (m-10) REVERT: I 50 THR cc_start: 0.8502 (t) cc_final: 0.8201 (m) REVERT: I 178 LYS cc_start: 0.8278 (tmtt) cc_final: 0.8053 (mtmm) REVERT: I 396 MET cc_start: 0.8720 (pmm) cc_final: 0.7681 (mtt) REVERT: I 426 MET cc_start: 0.7647 (mtt) cc_final: 0.7371 (mmt) REVERT: I 458 TYR cc_start: 0.8360 (t80) cc_final: 0.8060 (t80) REVERT: J 617 ARG cc_start: 0.7316 (mmt-90) cc_final: 0.5290 (ttp-170) REVERT: J 635 ILE cc_start: 0.8349 (mm) cc_final: 0.7987 (mm) REVERT: K 6 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: K 39 GLN cc_start: 0.8218 (tt0) cc_final: 0.7946 (tt0) REVERT: L 90 GLN cc_start: 0.9307 (pp30) cc_final: 0.8852 (pp30) outliers start: 54 outliers final: 45 residues processed: 345 average time/residue: 0.3113 time to fit residues: 161.9738 Evaluate side-chains 352 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 305 time to evaluate : 2.244 ------------------------------------------------------------------------------- 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 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 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 46 LEU 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 196 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 96 VAL 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 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 6 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 193 optimal weight: 0.0470 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 overall best weight: 2.2282 ------------------------------------------------------------------------------- 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** B 630 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.159312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.139744 restraints weight = 24054.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.137706 restraints weight = 38680.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.137418 restraints weight = 40015.492| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19458 Z= 0.289 Angle : 0.654 12.518 26406 Z= 0.343 Chirality : 0.046 0.248 2937 Planarity : 0.004 0.053 3378 Dihedral : 5.221 27.646 2637 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 2.52 % Allowed : 20.00 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2379 helix: 2.18 (0.28), residues: 363 sheet: -0.37 (0.20), residues: 714 loop : -1.04 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 35 HIS 0.011 0.002 HIS I 355 PHE 0.013 0.002 PHE E 361 TYR 0.018 0.002 TYR K 50 ARG 0.008 0.001 ARG E 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4144.84 seconds wall clock time: 76 minutes 31.33 seconds (4591.33 seconds total)