Starting phenix.real_space_refine on Thu Mar 21 02:16:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5p_13843/03_2024/7q5p_13843.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5p_13843/03_2024/7q5p_13843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5p_13843/03_2024/7q5p_13843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5p_13843/03_2024/7q5p_13843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5p_13843/03_2024/7q5p_13843.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5p_13843/03_2024/7q5p_13843.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 9276 2.51 5 N 2691 2.21 5 O 2853 1.98 5 H 14244 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29112 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9704 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 28, 'TRANS': 598} Chain breaks: 1 Chain: "B" Number of atoms: 9704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9704 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 28, 'TRANS': 598} Chain breaks: 1 Chain: "C" Number of atoms: 9704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9704 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 28, 'TRANS': 598} Chain breaks: 1 Time building chain proxies: 12.08, per 1000 atoms: 0.41 Number of scatterers: 29112 At special positions: 0 Unit cell: (90.2, 94.6, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 2853 8.00 N 2691 7.00 C 9276 6.00 H 14244 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 23.89 Conformation dependent library (CDL) restraints added in 3.2 seconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3426 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 22 sheets defined 14.8% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.689A pdb=" N LEU A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 264 through 283 removed outlier: 4.375A pdb=" N HIS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.689A pdb=" N LEU B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 264 through 283 removed outlier: 4.374A pdb=" N HIS B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.689A pdb=" N LEU C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 264 through 283 removed outlier: 4.374A pdb=" N HIS C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 8 through 10 current: chain 'A' and resid 31 through 41 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 31 through 41 current: chain 'A' and resid 67 through 69 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 67 through 69 current: chain 'A' and resid 87 through 89 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 87 through 89 current: chain 'A' and resid 284 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 290 current: chain 'A' and resid 314 through 325 removed outlier: 5.338A pdb=" N ILE A 317 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 347 " --> pdb=" O ILE A 317 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 339 through 348 current: chain 'B' and resid 31 through 41 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 31 through 41 current: chain 'B' and resid 67 through 69 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 67 through 69 current: chain 'B' and resid 87 through 89 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 87 through 89 current: chain 'B' and resid 284 through 290 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 290 current: chain 'B' and resid 314 through 325 removed outlier: 5.337A pdb=" N ILE B 317 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 347 " --> pdb=" O ILE B 317 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 339 through 348 current: chain 'C' and resid 31 through 41 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 31 through 41 current: chain 'C' and resid 67 through 69 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 67 through 69 current: chain 'C' and resid 87 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 87 through 89 current: chain 'C' and resid 284 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 290 current: chain 'C' and resid 314 through 325 removed outlier: 5.337A pdb=" N ILE C 317 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 347 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 113 removed outlier: 7.635A pdb=" N ASP A 105 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 148 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU A 142 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER A 113 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 140 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.809A pdb=" N GLU A 131 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.292A pdb=" N SER A 223 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP A 257 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU A 225 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASN A 227 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 392 removed outlier: 4.308A pdb=" N LYS A 389 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 430 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER A 434 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A 445 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 467 removed outlier: 5.724A pdb=" N LEU A 496 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL C 507 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 498 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 503 through 508 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 516 removed outlier: 3.629A pdb=" N ASN C 521 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS A 535 " --> pdb=" O GLU B 528 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL B 530 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 537 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE B 532 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 539 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS B 551 " --> pdb=" O ASP C 544 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 546 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU B 553 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL C 548 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER B 555 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR A 560 " --> pdb=" O ARG C 569 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 571 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C 584 " --> pdb=" O ASN C 580 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 591 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 512 through 516 removed outlier: 6.054A pdb=" N ASN A 521 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL B 516 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER A 523 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG A 520 " --> pdb=" O TYR C 529 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR C 531 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS A 522 " --> pdb=" O THR C 531 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS B 535 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL C 530 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR B 537 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE C 532 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 539 " --> pdb=" O ILE C 532 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 543 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ARG B 538 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU A 545 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL B 540 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 547 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 584 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.421A pdb=" N ASN A 591 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A 552 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS A 551 " --> pdb=" O ASP B 544 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU B 546 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU A 553 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 548 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER A 555 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 543 " --> pdb=" O ARG C 536 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ARG C 538 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU B 545 " --> pdb=" O ARG C 538 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL C 540 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 547 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN B 521 " --> pdb=" O HIS C 514 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL C 516 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER B 523 " --> pdb=" O VAL C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 601 through 602 removed outlier: 3.788A pdb=" N ILE A 602 " --> pdb=" O HIS C 609 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 610 removed outlier: 6.621A pdb=" N HIS A 609 " --> pdb=" O ILE B 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 104 through 113 removed outlier: 7.636A pdb=" N ASP B 105 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 148 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU B 142 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER B 113 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU B 140 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 130 through 132 removed outlier: 6.808A pdb=" N GLU B 131 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.292A pdb=" N SER B 223 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP B 257 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU B 225 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASN B 227 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 389 through 392 removed outlier: 4.308A pdb=" N LYS B 389 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU B 430 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER B 434 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 445 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 503 through 508 Processing sheet with id=AB9, first strand: chain 'B' and resid 609 through 610 removed outlier: 6.651A pdb=" N HIS B 609 " --> pdb=" O ILE C 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 104 through 113 removed outlier: 7.635A pdb=" N ASP C 105 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG C 148 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU C 142 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER C 113 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU C 140 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 132 removed outlier: 6.809A pdb=" N GLU C 131 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 240 through 243 removed outlier: 6.293A pdb=" N SER C 223 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP C 257 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU C 225 " --> pdb=" O ASP C 257 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASN C 227 " --> pdb=" O PRO C 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 389 through 392 removed outlier: 4.308A pdb=" N LYS C 389 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU C 430 " --> pdb=" O VAL C 449 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 434 " --> pdb=" O ILE C 445 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE C 445 " --> pdb=" O SER C 434 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 888 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: 11.99 Time building geometry restraints manager: 24.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14220 1.03 - 1.22: 24 1.22 - 1.42: 6687 1.42 - 1.61: 8445 1.61 - 1.81: 72 Bond restraints: 29448 Sorted by residual: bond pdb=" N LEU A 6 " pdb=" H LEU A 6 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" N LEU C 6 " pdb=" H LEU C 6 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" N LEU B 6 " pdb=" H LEU B 6 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" N ARG A 5 " pdb=" CA ARG A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ARG C 5 " pdb=" CA ARG C 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 29443 not shown) Histogram of bond angle deviations from ideal: 79.27 - 90.22: 12 90.22 - 101.18: 15 101.18 - 112.13: 32325 112.13 - 123.08: 16858 123.08 - 134.03: 3647 Bond angle restraints: 52857 Sorted by residual: angle pdb=" CG1 ILE A 562 " pdb=" CD1 ILE A 562 " pdb="HD12 ILE A 562 " ideal model delta sigma weight residual 109.00 79.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" CG1 ILE C 562 " pdb=" CD1 ILE C 562 " pdb="HD12 ILE C 562 " ideal model delta sigma weight residual 109.00 79.28 29.72 3.00e+00 1.11e-01 9.81e+01 angle pdb=" CG1 ILE B 562 " pdb=" CD1 ILE B 562 " pdb="HD12 ILE B 562 " ideal model delta sigma weight residual 109.00 79.34 29.66 3.00e+00 1.11e-01 9.78e+01 angle pdb=" CG1 ILE C 562 " pdb=" CD1 ILE C 562 " pdb="HD13 ILE C 562 " ideal model delta sigma weight residual 109.00 79.66 29.34 3.00e+00 1.11e-01 9.57e+01 angle pdb=" CG1 ILE A 562 " pdb=" CD1 ILE A 562 " pdb="HD13 ILE A 562 " ideal model delta sigma weight residual 109.00 79.66 29.34 3.00e+00 1.11e-01 9.56e+01 ... (remaining 52852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12460 17.87 - 35.74: 884 35.74 - 53.60: 319 53.60 - 71.47: 242 71.47 - 89.34: 30 Dihedral angle restraints: 13935 sinusoidal: 7572 harmonic: 6363 Sorted by residual: dihedral pdb=" CA TYR A 258 " pdb=" C TYR A 258 " pdb=" N PRO A 259 " pdb=" CA PRO A 259 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA TYR C 258 " pdb=" C TYR C 258 " pdb=" N PRO C 259 " pdb=" CA PRO C 259 " ideal model delta harmonic sigma weight residual 180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA TYR B 258 " pdb=" C TYR B 258 " pdb=" N PRO B 259 " pdb=" CA PRO B 259 " ideal model delta harmonic sigma weight residual -180.00 -149.96 -30.04 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 13932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1315 0.038 - 0.076: 619 0.076 - 0.114: 200 0.114 - 0.153: 20 0.153 - 0.191: 6 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA HIS B 609 " pdb=" N HIS B 609 " pdb=" C HIS B 609 " pdb=" CB HIS B 609 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA HIS A 609 " pdb=" N HIS A 609 " pdb=" C HIS A 609 " pdb=" CB HIS A 609 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CA HIS C 609 " pdb=" N HIS C 609 " pdb=" C HIS C 609 " pdb=" CB HIS C 609 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 2157 not shown) Planarity restraints: 4557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 107 " -0.069 9.50e-02 1.11e+02 4.36e-02 3.14e+01 pdb=" NE ARG B 107 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 107 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG B 107 " 0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG B 107 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG B 107 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 107 " -0.060 2.00e-02 2.50e+03 pdb="HH21 ARG B 107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 107 " 0.068 9.50e-02 1.11e+02 4.33e-02 3.11e+01 pdb=" NE ARG A 107 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 107 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG A 107 " -0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG A 107 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 107 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 107 " 0.060 2.00e-02 2.50e+03 pdb="HH21 ARG A 107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 107 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 107 " -0.069 9.50e-02 1.11e+02 4.34e-02 3.09e+01 pdb=" NE ARG C 107 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 107 " 0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG C 107 " 0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG C 107 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG C 107 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C 107 " -0.060 2.00e-02 2.50e+03 pdb="HH21 ARG C 107 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 107 " -0.021 2.00e-02 2.50e+03 ... (remaining 4554 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1640 2.16 - 2.77: 60254 2.77 - 3.38: 84782 3.38 - 3.99: 116021 3.99 - 4.60: 179456 Nonbonded interactions: 442153 Sorted by model distance: nonbonded pdb=" O LEU A 553 " pdb=" H LEU B 546 " model vdw 1.550 1.850 nonbonded pdb=" O LEU B 553 " pdb=" H LEU C 546 " model vdw 1.566 1.850 nonbonded pdb=" OE1 GLU A 563 " pdb=" HG SER B 555 " model vdw 1.567 1.850 nonbonded pdb=" OD1 ASN C 10 " pdb=" HG SER C 59 " model vdw 1.585 1.850 nonbonded pdb=" OD1 ASN B 10 " pdb=" HG SER B 59 " model vdw 1.586 1.850 ... (remaining 442148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.430 Extract box with map and model: 14.670 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 92.410 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 : 0.008 0.061 15204 Z= 0.496 Angle : 0.730 7.063 20601 Z= 0.402 Chirality : 0.047 0.191 2160 Planarity : 0.009 0.098 2766 Dihedral : 14.112 89.339 5622 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.22 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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: -2.06 (0.18), residues: 1869 helix: -2.30 (0.28), residues: 183 sheet: -1.55 (0.21), residues: 522 loop : -1.08 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP A 414 HIS 0.009 0.003 HIS B 209 PHE 0.023 0.003 PHE C 435 TYR 0.032 0.004 TYR B 143 ARG 0.025 0.003 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 VAL cc_start: 0.6843 (m) cc_final: 0.6577 (t) REVERT: A 463 ASN cc_start: 0.8446 (m-40) cc_final: 0.8244 (m110) REVERT: A 481 ASN cc_start: 0.8505 (m110) cc_final: 0.8295 (m-40) REVERT: B 316 LEU cc_start: 0.8460 (tp) cc_final: 0.8211 (tp) REVERT: B 384 GLN cc_start: 0.8075 (pm20) cc_final: 0.7691 (mp10) REVERT: B 463 ASN cc_start: 0.8513 (m-40) cc_final: 0.8257 (m110) REVERT: C 181 ASP cc_start: 0.7094 (p0) cc_final: 0.6813 (p0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.7802 time to fit residues: 284.1218 Evaluate side-chains 117 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN B 161 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15204 Z= 0.284 Angle : 0.671 7.732 20601 Z= 0.363 Chirality : 0.045 0.136 2160 Planarity : 0.005 0.044 2766 Dihedral : 7.198 27.523 2088 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.94 % Favored : 93.90 % Rotamer: Outliers : 1.57 % Allowed : 8.60 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1869 helix: -1.19 (0.32), residues: 216 sheet: -1.93 (0.20), residues: 528 loop : -0.78 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 213 HIS 0.006 0.001 HIS B 209 PHE 0.014 0.002 PHE C 435 TYR 0.015 0.001 TYR A 138 ARG 0.009 0.001 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ASN cc_start: 0.8506 (m110) cc_final: 0.8234 (m-40) REVERT: B 153 ASP cc_start: 0.8674 (m-30) cc_final: 0.8473 (m-30) REVERT: B 312 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6873 (m-40) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.6792 time to fit residues: 144.9772 Evaluate side-chains 123 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 161 GLN ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN B 626 GLN C 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15204 Z= 0.264 Angle : 0.605 7.045 20601 Z= 0.325 Chirality : 0.044 0.132 2160 Planarity : 0.004 0.047 2766 Dihedral : 6.594 26.843 2088 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.82 % Allowed : 8.73 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.19), residues: 1869 helix: -0.56 (0.35), residues: 207 sheet: -1.81 (0.20), residues: 540 loop : -0.71 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 213 HIS 0.007 0.001 HIS C 360 PHE 0.011 0.002 PHE A 306 TYR 0.016 0.001 TYR A 143 ARG 0.005 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.6056 (OUTLIER) cc_final: 0.5552 (pp30) REVERT: A 291 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7253 (m-40) REVERT: A 481 ASN cc_start: 0.8417 (m110) cc_final: 0.8138 (m-40) REVERT: B 153 ASP cc_start: 0.8660 (m-30) cc_final: 0.8415 (m-30) REVERT: B 291 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.7168 (m-40) REVERT: B 312 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6840 (m-40) REVERT: C 270 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6879 (t-90) outliers start: 45 outliers final: 23 residues processed: 139 average time/residue: 0.5928 time to fit residues: 122.6369 Evaluate side-chains 127 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15204 Z= 0.313 Angle : 0.620 7.222 20601 Z= 0.332 Chirality : 0.044 0.133 2160 Planarity : 0.004 0.041 2766 Dihedral : 6.458 26.742 2088 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.08 % Allowed : 9.23 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.19), residues: 1869 helix: -0.37 (0.36), residues: 207 sheet: -1.97 (0.20), residues: 543 loop : -0.85 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 213 HIS 0.005 0.001 HIS B 209 PHE 0.013 0.002 PHE A 306 TYR 0.016 0.001 TYR A 138 ARG 0.004 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 105 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.5886 (OUTLIER) cc_final: 0.5333 (pp30) REVERT: A 291 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7386 (m-40) REVERT: A 481 ASN cc_start: 0.8452 (m110) cc_final: 0.8141 (m-40) REVERT: B 153 ASP cc_start: 0.8672 (m-30) cc_final: 0.8435 (m-30) REVERT: B 291 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7306 (m-40) REVERT: B 312 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6979 (m-40) outliers start: 49 outliers final: 35 residues processed: 135 average time/residue: 0.6093 time to fit residues: 122.4020 Evaluate side-chains 132 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 93 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 161 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15204 Z= 0.321 Angle : 0.614 7.243 20601 Z= 0.329 Chirality : 0.044 0.138 2160 Planarity : 0.004 0.038 2766 Dihedral : 6.327 26.950 2088 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.08 % Allowed : 9.98 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.19), residues: 1869 helix: -0.25 (0.37), residues: 207 sheet: -2.08 (0.21), residues: 522 loop : -0.94 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 213 HIS 0.005 0.001 HIS C 609 PHE 0.013 0.002 PHE C 33 TYR 0.013 0.001 TYR A 143 ARG 0.003 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 102 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.5851 (OUTLIER) cc_final: 0.5311 (pp30) REVERT: A 291 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7483 (m-40) REVERT: A 481 ASN cc_start: 0.8449 (m110) cc_final: 0.8128 (m-40) REVERT: B 153 ASP cc_start: 0.8676 (m-30) cc_final: 0.8418 (m-30) REVERT: B 291 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7407 (m-40) REVERT: B 312 ASN cc_start: 0.7229 (OUTLIER) cc_final: 0.6990 (m-40) REVERT: C 541 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7586 (mt0) outliers start: 49 outliers final: 34 residues processed: 133 average time/residue: 0.7794 time to fit residues: 151.9255 Evaluate side-chains 131 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 570 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 0.1980 chunk 83 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15204 Z= 0.205 Angle : 0.560 6.443 20601 Z= 0.295 Chirality : 0.043 0.132 2160 Planarity : 0.004 0.037 2766 Dihedral : 5.957 25.500 2088 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.57 % Allowed : 10.61 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 1869 helix: 0.11 (0.38), residues: 207 sheet: -1.99 (0.21), residues: 522 loop : -0.76 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 213 HIS 0.004 0.001 HIS A 209 PHE 0.010 0.001 PHE B 33 TYR 0.012 0.001 TYR A 143 ARG 0.003 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 102 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7428 (m-40) REVERT: A 481 ASN cc_start: 0.8376 (m110) cc_final: 0.8056 (m-40) REVERT: B 153 ASP cc_start: 0.8590 (m-30) cc_final: 0.8247 (m-30) REVERT: B 291 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7430 (m-40) REVERT: B 312 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6886 (m-40) REVERT: B 555 SER cc_start: 0.7830 (m) cc_final: 0.7610 (t) outliers start: 41 outliers final: 35 residues processed: 124 average time/residue: 0.6556 time to fit residues: 118.5015 Evaluate side-chains 133 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 95 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15204 Z= 0.306 Angle : 0.599 8.695 20601 Z= 0.318 Chirality : 0.043 0.136 2160 Planarity : 0.004 0.036 2766 Dihedral : 6.035 25.296 2088 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.39 % Allowed : 10.11 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.19), residues: 1869 helix: 0.15 (0.37), residues: 207 sheet: -2.09 (0.21), residues: 522 loop : -0.89 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 213 HIS 0.005 0.001 HIS A 209 PHE 0.012 0.002 PHE B 33 TYR 0.012 0.001 TYR A 138 ARG 0.003 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 100 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7493 (m-40) REVERT: A 481 ASN cc_start: 0.8433 (m110) cc_final: 0.8114 (m-40) REVERT: A 610 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8187 (mt) REVERT: B 153 ASP cc_start: 0.8614 (m-30) cc_final: 0.8288 (m-30) REVERT: B 291 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7553 (m-40) REVERT: B 312 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.7027 (m-40) REVERT: B 555 SER cc_start: 0.7947 (m) cc_final: 0.7716 (t) REVERT: B 610 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8173 (mt) REVERT: C 610 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8197 (mt) outliers start: 54 outliers final: 46 residues processed: 132 average time/residue: 0.6625 time to fit residues: 126.1989 Evaluate side-chains 147 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 95 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 140 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15204 Z= 0.179 Angle : 0.560 11.084 20601 Z= 0.291 Chirality : 0.043 0.129 2160 Planarity : 0.003 0.037 2766 Dihedral : 5.782 24.818 2088 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.89 % Allowed : 10.86 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1869 helix: 0.49 (0.39), residues: 207 sheet: -2.03 (0.21), residues: 522 loop : -0.71 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 213 HIS 0.018 0.001 HIS A 360 PHE 0.010 0.001 PHE C 637 TYR 0.012 0.001 TYR C 143 ARG 0.004 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 98 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7559 (m-40) REVERT: A 481 ASN cc_start: 0.8315 (m110) cc_final: 0.7989 (m-40) REVERT: B 153 ASP cc_start: 0.8589 (m-30) cc_final: 0.8258 (m-30) REVERT: B 291 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7240 (m-40) REVERT: B 312 ASN cc_start: 0.7120 (OUTLIER) cc_final: 0.6894 (m-40) REVERT: B 555 SER cc_start: 0.7853 (m) cc_final: 0.7626 (t) REVERT: B 610 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8118 (mt) REVERT: C 143 TYR cc_start: 0.8279 (t80) cc_final: 0.7958 (t80) REVERT: C 610 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8144 (mt) outliers start: 46 outliers final: 35 residues processed: 124 average time/residue: 0.6890 time to fit residues: 122.4945 Evaluate side-chains 138 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 610 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 chunk 166 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15204 Z= 0.225 Angle : 0.565 10.830 20601 Z= 0.294 Chirality : 0.043 0.129 2160 Planarity : 0.004 0.034 2766 Dihedral : 5.710 24.267 2088 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.01 % Allowed : 10.92 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1869 helix: 0.59 (0.39), residues: 207 sheet: -2.05 (0.21), residues: 522 loop : -0.72 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 213 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE B 211 TYR 0.011 0.001 TYR A 143 ARG 0.003 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 100 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7636 (m-40) REVERT: A 481 ASN cc_start: 0.8386 (m110) cc_final: 0.8051 (m-40) REVERT: A 610 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8174 (mt) REVERT: B 153 ASP cc_start: 0.8594 (m-30) cc_final: 0.8263 (m-30) REVERT: B 312 ASN cc_start: 0.7163 (OUTLIER) cc_final: 0.6927 (m-40) REVERT: B 321 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7826 (mmm160) REVERT: B 555 SER cc_start: 0.7957 (m) cc_final: 0.7726 (t) REVERT: B 610 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8160 (mt) REVERT: C 143 TYR cc_start: 0.8287 (t80) cc_final: 0.7960 (t80) REVERT: C 610 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8185 (mt) outliers start: 48 outliers final: 38 residues processed: 130 average time/residue: 0.6763 time to fit residues: 125.9363 Evaluate side-chains 141 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 98 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 610 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 185 optimal weight: 0.0050 chunk 170 optimal weight: 1.9990 chunk 147 optimal weight: 0.0770 chunk 15 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15204 Z= 0.148 Angle : 0.538 10.010 20601 Z= 0.276 Chirality : 0.043 0.129 2160 Planarity : 0.003 0.037 2766 Dihedral : 5.417 23.821 2088 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.32 % Allowed : 11.61 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1869 helix: 0.84 (0.40), residues: 207 sheet: -1.92 (0.22), residues: 528 loop : -0.54 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 394 HIS 0.004 0.001 HIS A 209 PHE 0.009 0.001 PHE A 167 TYR 0.012 0.001 TYR C 143 ARG 0.004 0.000 ARG C 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 112 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ASN cc_start: 0.8330 (m110) cc_final: 0.7990 (m-40) REVERT: A 610 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8144 (mt) REVERT: B 143 TYR cc_start: 0.8399 (t80) cc_final: 0.8155 (t80) REVERT: B 153 ASP cc_start: 0.8562 (m-30) cc_final: 0.8250 (m-30) REVERT: B 312 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6879 (m-40) REVERT: B 555 SER cc_start: 0.7844 (m) cc_final: 0.7618 (t) REVERT: B 610 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8203 (mt) REVERT: C 143 TYR cc_start: 0.8266 (t80) cc_final: 0.7941 (t80) REVERT: C 610 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8146 (mt) outliers start: 37 outliers final: 28 residues processed: 132 average time/residue: 0.6642 time to fit residues: 127.1819 Evaluate side-chains 131 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 610 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.105506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.092176 restraints weight = 74676.305| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.41 r_work: 0.3718 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15204 Z= 0.238 Angle : 0.562 10.668 20601 Z= 0.291 Chirality : 0.043 0.131 2160 Planarity : 0.003 0.034 2766 Dihedral : 5.534 23.434 2088 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.51 % Allowed : 11.24 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1869 helix: 0.81 (0.40), residues: 207 sheet: -2.02 (0.22), residues: 528 loop : -0.65 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 213 HIS 0.004 0.001 HIS A 209 PHE 0.010 0.001 PHE B 33 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG C 321 =============================================================================== Job complete usr+sys time: 6253.68 seconds wall clock time: 111 minutes 30.16 seconds (6690.16 seconds total)