Starting phenix.real_space_refine on Sat Jun 29 19:32:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh2_19166/06_2024/8rh2_19166.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh2_19166/06_2024/8rh2_19166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh2_19166/06_2024/8rh2_19166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh2_19166/06_2024/8rh2_19166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh2_19166/06_2024/8rh2_19166.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh2_19166/06_2024/8rh2_19166.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 12036 2.51 5 N 3390 2.21 5 O 3630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B GLU 646": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 59": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 19152 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4710 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "B" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4710 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "C" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4710 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 10.33, per 1000 atoms: 0.54 Number of scatterers: 19152 At special positions: 0 Unit cell: (190.565, 169.963, 160.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3630 8.00 N 3390 7.00 C 12036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 567 " distance=2.04 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 523 " distance=2.06 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 263 " distance=2.04 Simple disulfide: pdb=" SG CYS A 356 " - pdb=" SG CYS A 404 " distance=2.04 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 627 " distance=2.05 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 567 " distance=2.04 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 523 " distance=2.08 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 263 " distance=2.04 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 404 " distance=2.03 Simple disulfide: pdb=" SG CYS B 590 " - pdb=" SG CYS B 627 " distance=2.05 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 567 " distance=2.05 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 523 " distance=2.07 Simple disulfide: pdb=" SG CYS C 199 " - pdb=" SG CYS C 263 " distance=2.04 Simple disulfide: pdb=" SG CYS C 356 " - pdb=" SG CYS C 404 " distance=2.04 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 627 " distance=2.05 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 101 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 101 " distance=2.04 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: 7.39 Conformation dependent library (CDL) restraints added in 3.3 seconds 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 49 sheets defined 18.5% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.653A pdb=" N THR A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 402 through 420 removed outlier: 4.643A pdb=" N GLY A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 540 removed outlier: 4.085A pdb=" N GLY A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 695 through 704 Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 402 through 421 removed outlier: 4.389A pdb=" N GLY B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 540 removed outlier: 4.279A pdb=" N THR B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 550 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 695 through 704 Processing helix chain 'B' and resid 705 through 711 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.520A pdb=" N THR C 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 302 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 495 through 540 removed outlier: 4.368A pdb=" N THR C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 550 removed outlier: 3.734A pdb=" N ILE C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 654 through 658 removed outlier: 3.523A pdb=" N VAL C 658 " --> pdb=" O ARG C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 695 through 705 Processing helix chain 'C' and resid 705 through 711 removed outlier: 3.503A pdb=" N ALA C 711 " --> pdb=" O ASP C 707 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.530A pdb=" N GLN H 70 " --> pdb=" O ARG H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 92 through 95 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.892A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.753A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.751A pdb=" N GLU G 82 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 70 removed outlier: 3.718A pdb=" N GLN D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 67 through 70' Processing helix chain 'D' and resid 92 through 95 Processing helix chain 'F' and resid 67 through 70 removed outlier: 3.618A pdb=" N GLN F 70 " --> pdb=" O ARG F 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 70' Processing helix chain 'F' and resid 92 through 95 Processing sheet with id=AA1, first strand: chain 'A' and resid 568 through 570 removed outlier: 7.551A pdb=" N TYR A 106 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 553 through 557 removed outlier: 6.687A pdb=" N VAL A 116 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 661 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN A 118 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 364 removed outlier: 5.356A pdb=" N LYS A 360 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS A 143 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 364 removed outlier: 5.356A pdb=" N LYS A 360 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS A 143 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 183 removed outlier: 6.326A pdb=" N GLN A 164 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 177 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 162 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 179 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 160 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 181 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS A 158 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TYR A 156 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 227 through 228 removed outlier: 7.190A pdb=" N LYS A 152 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 347 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N THR A 332 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 316 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA9, first strand: chain 'A' and resid 202 through 207 Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB2, first strand: chain 'A' and resid 632 through 637 removed outlier: 6.919A pdb=" N TYR A 641 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLN A 652 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR A 643 " --> pdb=" O SER A 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 659 through 661 removed outlier: 3.997A pdb=" N THR A 659 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 568 through 570 removed outlier: 7.636A pdb=" N TYR B 106 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 364 removed outlier: 5.374A pdb=" N LYS B 360 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS B 143 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 358 through 364 removed outlier: 5.374A pdb=" N LYS B 360 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS B 143 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 183 removed outlier: 6.413A pdb=" N GLN B 164 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE B 177 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 162 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU B 179 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 160 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG B 181 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS B 158 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N TYR B 156 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 227 through 228 removed outlier: 7.196A pdb=" N LYS B 152 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP B 347 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR B 332 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 316 " --> pdb=" O THR B 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AC1, first strand: chain 'B' and resid 202 through 207 Processing sheet with id=AC2, first strand: chain 'B' and resid 367 through 372 Processing sheet with id=AC3, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AC4, first strand: chain 'B' and resid 632 through 637 removed outlier: 5.245A pdb=" N GLU B 645 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 659 through 661 removed outlier: 3.918A pdb=" N THR B 659 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 568 through 570 removed outlier: 7.389A pdb=" N TYR C 106 " --> pdb=" O LEU C 617 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 358 through 364 removed outlier: 5.266A pdb=" N LYS C 360 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS C 143 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 364 removed outlier: 5.266A pdb=" N LYS C 360 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS C 143 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 172 through 183 removed outlier: 6.135A pdb=" N GLN C 164 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE C 177 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 162 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU C 179 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL C 160 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 181 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS C 158 " --> pdb=" O ARG C 181 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N TYR C 156 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 227 through 228 removed outlier: 7.062A pdb=" N LYS C 152 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP C 347 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR C 332 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 316 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AD3, first strand: chain 'C' and resid 202 through 206 Processing sheet with id=AD4, first strand: chain 'C' and resid 367 through 372 Processing sheet with id=AD5, first strand: chain 'C' and resid 589 through 591 Processing sheet with id=AD6, first strand: chain 'C' and resid 632 through 637 removed outlier: 5.231A pdb=" N GLU C 645 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 8 through 11 Processing sheet with id=AD8, first strand: chain 'H' and resid 15 through 16 removed outlier: 6.644A pdb=" N GLU H 15 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE H 39 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.537A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AE3, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.628A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AE5, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AE6, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.645A pdb=" N VAL G 10 " --> pdb=" O THR G 104 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.645A pdb=" N VAL G 10 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE9, first strand: chain 'D' and resid 8 through 11 Processing sheet with id=AF1, first strand: chain 'D' and resid 15 through 16 removed outlier: 6.659A pdb=" N GLU D 15 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA D 45 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU D 50 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 8 through 11 Processing sheet with id=AF3, first strand: chain 'F' and resid 15 through 16 removed outlier: 5.823A pdb=" N ARG F 43 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TRP F 52 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA F 45 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU F 50 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 15 through 16 removed outlier: 4.467A pdb=" N VAL F 116 " --> pdb=" O ARG F 103 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2250 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: 7.29 Time building geometry restraints manager: 8.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6357 1.34 - 1.47: 5049 1.47 - 1.59: 8058 1.59 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 19614 Sorted by residual: bond pdb=" CE1 HIS D 32 " pdb=" NE2 HIS D 32 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS H 32 " pdb=" NE2 HIS H 32 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.26e+01 bond pdb=" CE1 HIS C 220 " pdb=" NE2 HIS C 220 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.12e+01 bond pdb=" CE1 HIS C 169 " pdb=" NE2 HIS C 169 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.12e+01 bond pdb=" CE1 HIS B 220 " pdb=" NE2 HIS B 220 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 ... (remaining 19609 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.47: 400 105.47 - 112.64: 10069 112.64 - 119.81: 6277 119.81 - 126.98: 9645 126.98 - 134.15: 252 Bond angle restraints: 26643 Sorted by residual: angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 113.53 110.76 2.77 9.80e-01 1.04e+00 8.00e+00 angle pdb=" C SER G 92 " pdb=" CA SER G 92 " pdb=" CB SER G 92 " ideal model delta sigma weight residual 110.42 115.98 -5.56 1.99e+00 2.53e-01 7.80e+00 angle pdb=" C TYR G 49 " pdb=" N ASP G 50 " pdb=" CA ASP G 50 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 angle pdb=" N VAL G 95 " pdb=" CA VAL G 95 " pdb=" CB VAL G 95 " ideal model delta sigma weight residual 111.00 113.73 -2.73 1.14e+00 7.69e-01 5.73e+00 angle pdb=" C TYR L 49 " pdb=" N ASP L 50 " pdb=" CA ASP L 50 " ideal model delta sigma weight residual 121.54 125.98 -4.44 1.91e+00 2.74e-01 5.41e+00 ... (remaining 26638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10543 17.96 - 35.92: 854 35.92 - 53.89: 176 53.89 - 71.85: 47 71.85 - 89.81: 26 Dihedral angle restraints: 11646 sinusoidal: 4638 harmonic: 7008 Sorted by residual: dihedral pdb=" CB CYS C 590 " pdb=" SG CYS C 590 " pdb=" SG CYS C 627 " pdb=" CB CYS C 627 " ideal model delta sinusoidal sigma weight residual -86.00 -169.93 83.93 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS B 590 " pdb=" SG CYS B 590 " pdb=" SG CYS B 627 " pdb=" CB CYS B 627 " ideal model delta sinusoidal sigma weight residual -86.00 -169.36 83.36 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A 590 " pdb=" SG CYS A 590 " pdb=" SG CYS A 627 " pdb=" CB CYS A 627 " ideal model delta sinusoidal sigma weight residual -86.00 -168.51 82.51 1 1.00e+01 1.00e-02 8.35e+01 ... (remaining 11643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1809 0.040 - 0.081: 821 0.081 - 0.121: 224 0.121 - 0.161: 34 0.161 - 0.202: 1 Chirality restraints: 2889 Sorted by residual: chirality pdb=" CB VAL L 95 " pdb=" CA VAL L 95 " pdb=" CG1 VAL L 95 " pdb=" CG2 VAL L 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU B 297 " pdb=" N GLU B 297 " pdb=" C GLU B 297 " pdb=" CB GLU B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CB VAL G 95 " pdb=" CA VAL G 95 " pdb=" CG1 VAL G 95 " pdb=" CG2 VAL G 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 2886 not shown) Planarity restraints: 3477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 48 " 0.016 2.00e-02 2.50e+03 1.66e-02 5.48e+00 pdb=" CG TYR E 48 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 48 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 48 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 48 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR E 48 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 48 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR E 48 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 568 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 569 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 569 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 569 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 509 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C ARG A 509 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG A 509 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS A 510 " -0.012 2.00e-02 2.50e+03 ... (remaining 3474 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1589 2.74 - 3.28: 17858 3.28 - 3.82: 32252 3.82 - 4.36: 39371 4.36 - 4.90: 69166 Nonbonded interactions: 160236 Sorted by model distance: nonbonded pdb=" OH TYR C 274 " pdb=" OD2 ASP C 400 " model vdw 2.205 2.440 nonbonded pdb=" O THR A 135 " pdb=" OH TYR A 444 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR A 157 " pdb=" OE2 GLU A 266 " model vdw 2.213 2.440 nonbonded pdb=" NH1 ARG B 655 " pdb=" OE1 GLN C 118 " model vdw 2.235 2.520 nonbonded pdb=" O THR B 135 " pdb=" OH TYR B 444 " model vdw 2.251 2.440 ... (remaining 160231 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' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.020 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 52.880 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.005 0.048 19614 Z= 0.330 Angle : 0.577 6.797 26643 Z= 0.339 Chirality : 0.047 0.202 2889 Planarity : 0.006 0.076 3477 Dihedral : 14.367 89.810 7107 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.05 % Allowed : 0.63 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.07 (0.16), residues: 2397 helix: 0.44 (0.29), residues: 312 sheet: 0.14 (0.17), residues: 834 loop : 0.02 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 533 HIS 0.015 0.003 HIS C 506 PHE 0.019 0.003 PHE H 34 TYR 0.039 0.003 TYR E 48 ARG 0.021 0.002 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.6519 (mtm-85) cc_final: 0.5935 (mtp85) REVERT: A 187 GLU cc_start: 0.7811 (pp20) cc_final: 0.6770 (pp20) REVERT: A 430 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8278 (mm110) REVERT: B 170 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7084 (mmt180) REVERT: B 421 TYR cc_start: 0.7806 (m-80) cc_final: 0.7570 (m-80) REVERT: C 136 GLU cc_start: 0.8318 (tp30) cc_final: 0.8086 (tp30) REVERT: C 175 MET cc_start: 0.9309 (mmt) cc_final: 0.8593 (mmt) REVERT: C 210 MET cc_start: 0.9282 (ttt) cc_final: 0.8673 (ttt) REVERT: C 578 GLN cc_start: 0.7440 (mp10) cc_final: 0.7194 (mp10) REVERT: D 38 ASP cc_start: 0.8566 (m-30) cc_final: 0.8361 (m-30) REVERT: D 62 ASN cc_start: 0.9129 (m-40) cc_final: 0.8470 (m-40) REVERT: D 95 ASP cc_start: 0.8667 (m-30) cc_final: 0.7945 (m-30) REVERT: F 78 ASN cc_start: 0.7616 (t0) cc_final: 0.7292 (t0) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.3623 time to fit residues: 151.3032 Evaluate side-chains 244 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 2.9990 chunk 179 optimal weight: 0.0010 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 112 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 303 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 GLN G 68 ASN D 68 GLN D 119 GLN F 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19614 Z= 0.176 Angle : 0.471 5.346 26643 Z= 0.255 Chirality : 0.042 0.170 2889 Planarity : 0.004 0.041 3477 Dihedral : 3.961 18.335 2715 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.68 % Allowed : 6.09 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.29 (0.17), residues: 2397 helix: 1.02 (0.29), residues: 327 sheet: 0.11 (0.17), residues: 870 loop : 0.18 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 533 HIS 0.010 0.001 HIS B 528 PHE 0.016 0.001 PHE C 279 TYR 0.026 0.001 TYR E 48 ARG 0.005 0.000 ARG B 618 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 247 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7564 (t70) cc_final: 0.7152 (t70) REVERT: A 187 GLU cc_start: 0.7687 (pp20) cc_final: 0.6816 (pp20) REVERT: A 191 ASP cc_start: 0.8544 (m-30) cc_final: 0.8271 (m-30) REVERT: C 175 MET cc_start: 0.9327 (mmt) cc_final: 0.8794 (mmt) REVERT: C 210 MET cc_start: 0.9297 (ttt) cc_final: 0.8716 (ttt) REVERT: C 578 GLN cc_start: 0.7439 (mp10) cc_final: 0.7157 (mp10) REVERT: H 51 GLU cc_start: 0.8183 (tt0) cc_final: 0.7893 (tt0) REVERT: D 38 ASP cc_start: 0.8525 (m-30) cc_final: 0.8298 (m-30) REVERT: D 62 ASN cc_start: 0.9108 (m-40) cc_final: 0.8443 (m110) REVERT: D 95 ASP cc_start: 0.8363 (m-30) cc_final: 0.7729 (m-30) REVERT: F 78 ASN cc_start: 0.7483 (t0) cc_final: 0.7028 (t0) outliers start: 14 outliers final: 12 residues processed: 260 average time/residue: 0.3484 time to fit residues: 132.9283 Evaluate side-chains 254 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 179 optimal weight: 0.2980 chunk 146 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN D 62 ASN F 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19614 Z= 0.202 Angle : 0.466 4.887 26643 Z= 0.252 Chirality : 0.042 0.179 2889 Planarity : 0.004 0.044 3477 Dihedral : 3.917 18.612 2715 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.22 % Allowed : 7.80 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.38 (0.17), residues: 2397 helix: 1.13 (0.29), residues: 327 sheet: 0.24 (0.17), residues: 855 loop : 0.15 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 52 HIS 0.009 0.001 HIS A 631 PHE 0.017 0.001 PHE C 279 TYR 0.026 0.001 TYR L 48 ARG 0.008 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7576 (t70) cc_final: 0.7132 (t70) REVERT: A 187 GLU cc_start: 0.7806 (pp20) cc_final: 0.7429 (pm20) REVERT: A 191 ASP cc_start: 0.8632 (m-30) cc_final: 0.8375 (m-30) REVERT: A 421 TYR cc_start: 0.7775 (m-10) cc_final: 0.7087 (m-10) REVERT: C 175 MET cc_start: 0.9322 (mmt) cc_final: 0.8783 (mmt) REVERT: C 210 MET cc_start: 0.9325 (ttt) cc_final: 0.8780 (ttt) REVERT: C 591 TYR cc_start: 0.7032 (m-10) cc_final: 0.6767 (m-10) REVERT: H 51 GLU cc_start: 0.8225 (tt0) cc_final: 0.7984 (tt0) REVERT: H 75 MET cc_start: 0.8210 (mtt) cc_final: 0.7731 (mtt) REVERT: D 38 ASP cc_start: 0.8504 (m-30) cc_final: 0.8235 (m-30) REVERT: D 62 ASN cc_start: 0.9108 (m110) cc_final: 0.8443 (m110) REVERT: D 95 ASP cc_start: 0.8329 (m-30) cc_final: 0.7682 (m-30) REVERT: F 78 ASN cc_start: 0.7733 (t0) cc_final: 0.7302 (t0) outliers start: 25 outliers final: 21 residues processed: 267 average time/residue: 0.3589 time to fit residues: 141.4068 Evaluate side-chains 258 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 205 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN A 668 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN C 240 HIS ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 HIS H 40 ASN G 26 ASN G 68 ASN F 8 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19614 Z= 0.332 Angle : 0.518 5.853 26643 Z= 0.280 Chirality : 0.044 0.234 2889 Planarity : 0.004 0.043 3477 Dihedral : 4.125 17.343 2715 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.90 % Allowed : 8.67 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.29 (0.17), residues: 2397 helix: 1.12 (0.29), residues: 324 sheet: 0.17 (0.17), residues: 858 loop : 0.09 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 52 HIS 0.009 0.001 HIS B 528 PHE 0.023 0.002 PHE C 279 TYR 0.039 0.002 TYR L 48 ARG 0.006 0.001 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 240 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: B 133 ASN cc_start: 0.8131 (m110) cc_final: 0.7910 (m-40) REVERT: B 644 PHE cc_start: 0.8153 (m-10) cc_final: 0.7938 (m-10) REVERT: C 175 MET cc_start: 0.9327 (mmt) cc_final: 0.8787 (mmt) REVERT: C 210 MET cc_start: 0.9366 (ttt) cc_final: 0.8827 (ttt) REVERT: C 416 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8322 (ptp) REVERT: H 17 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7396 (mmtp) REVERT: H 75 MET cc_start: 0.8611 (mtt) cc_final: 0.8261 (mtt) REVERT: D 38 ASP cc_start: 0.8565 (m-30) cc_final: 0.8323 (m-30) REVERT: D 62 ASN cc_start: 0.9166 (m110) cc_final: 0.8540 (m110) REVERT: D 95 ASP cc_start: 0.8425 (m-30) cc_final: 0.7565 (m-30) REVERT: F 78 ASN cc_start: 0.7814 (t0) cc_final: 0.7257 (t0) outliers start: 39 outliers final: 29 residues processed: 270 average time/residue: 0.3408 time to fit residues: 135.4670 Evaluate side-chains 262 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 170 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 HIS G 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19614 Z= 0.226 Angle : 0.472 5.021 26643 Z= 0.256 Chirality : 0.042 0.199 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.011 16.543 2715 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.51 % Allowed : 9.89 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.32 (0.17), residues: 2397 helix: 1.12 (0.29), residues: 327 sheet: 0.17 (0.17), residues: 846 loop : 0.14 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 533 HIS 0.008 0.001 HIS B 528 PHE 0.017 0.001 PHE C 279 TYR 0.031 0.001 TYR L 48 ARG 0.007 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 2.360 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7718 (pp20) cc_final: 0.7514 (pp20) REVERT: B 133 ASN cc_start: 0.8103 (m110) cc_final: 0.7888 (m-40) REVERT: B 644 PHE cc_start: 0.8163 (m-10) cc_final: 0.7927 (m-10) REVERT: C 175 MET cc_start: 0.9335 (mmt) cc_final: 0.8855 (mmt) REVERT: C 210 MET cc_start: 0.9346 (ttt) cc_final: 0.9081 (ttt) REVERT: C 416 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8411 (ptp) REVERT: H 17 LYS cc_start: 0.7800 (mmmt) cc_final: 0.7392 (mmtp) REVERT: H 51 GLU cc_start: 0.8339 (tt0) cc_final: 0.8117 (tt0) REVERT: H 75 MET cc_start: 0.8602 (mtt) cc_final: 0.8240 (mtt) REVERT: L 5 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8550 (t) REVERT: D 38 ASP cc_start: 0.8536 (m-30) cc_final: 0.8297 (m-30) REVERT: D 62 ASN cc_start: 0.9085 (m110) cc_final: 0.8445 (m110) REVERT: D 95 ASP cc_start: 0.8352 (m-30) cc_final: 0.7508 (m-30) REVERT: F 78 ASN cc_start: 0.7828 (t0) cc_final: 0.7241 (t0) outliers start: 31 outliers final: 25 residues processed: 265 average time/residue: 0.3413 time to fit residues: 132.5040 Evaluate side-chains 260 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 233 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 229 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 19 optimal weight: 0.0060 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19614 Z= 0.213 Angle : 0.464 4.997 26643 Z= 0.252 Chirality : 0.042 0.188 2889 Planarity : 0.004 0.041 3477 Dihedral : 3.963 16.304 2715 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.14 % Allowed : 9.80 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.34 (0.17), residues: 2397 helix: 1.15 (0.29), residues: 327 sheet: 0.09 (0.17), residues: 861 loop : 0.22 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.007 0.001 HIS A 631 PHE 0.017 0.001 PHE C 279 TYR 0.029 0.001 TYR L 48 ARG 0.007 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 2.189 Fit side-chains revert: symmetry clash REVERT: B 133 ASN cc_start: 0.8085 (m110) cc_final: 0.7872 (m-40) REVERT: B 366 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8273 (mt-10) REVERT: B 644 PHE cc_start: 0.8168 (m-10) cc_final: 0.7922 (m-10) REVERT: C 175 MET cc_start: 0.9344 (mmt) cc_final: 0.8891 (mmt) REVERT: C 210 MET cc_start: 0.9334 (ttt) cc_final: 0.9065 (ttt) REVERT: C 416 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8423 (ptp) REVERT: H 17 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7388 (mmtp) REVERT: H 51 GLU cc_start: 0.8331 (tt0) cc_final: 0.8111 (tt0) REVERT: H 75 MET cc_start: 0.8634 (mtt) cc_final: 0.8262 (mtt) REVERT: L 5 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8540 (t) REVERT: D 38 ASP cc_start: 0.8477 (m-30) cc_final: 0.8213 (m-30) REVERT: D 62 ASN cc_start: 0.9077 (m110) cc_final: 0.8429 (m110) REVERT: D 95 ASP cc_start: 0.8343 (m-30) cc_final: 0.7650 (m-30) REVERT: F 78 ASN cc_start: 0.7792 (t0) cc_final: 0.7196 (t0) outliers start: 44 outliers final: 35 residues processed: 275 average time/residue: 0.3465 time to fit residues: 140.9214 Evaluate side-chains 274 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 228 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19614 Z= 0.218 Angle : 0.467 6.001 26643 Z= 0.253 Chirality : 0.042 0.189 2889 Planarity : 0.004 0.041 3477 Dihedral : 3.946 16.010 2715 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.58 % Allowed : 9.94 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.37 (0.17), residues: 2397 helix: 1.16 (0.29), residues: 327 sheet: 0.20 (0.17), residues: 846 loop : 0.16 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 533 HIS 0.007 0.001 HIS A 631 PHE 0.017 0.001 PHE C 279 TYR 0.028 0.001 TYR L 48 ARG 0.008 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 238 time to evaluate : 2.036 Fit side-chains REVERT: A 104 GLN cc_start: 0.7060 (tt0) cc_final: 0.6745 (tt0) REVERT: B 133 ASN cc_start: 0.8236 (m110) cc_final: 0.8033 (m-40) REVERT: B 269 ASP cc_start: 0.8420 (m-30) cc_final: 0.7913 (t70) REVERT: B 644 PHE cc_start: 0.8166 (m-10) cc_final: 0.7905 (m-10) REVERT: C 175 MET cc_start: 0.9344 (mmt) cc_final: 0.8876 (mmt) REVERT: C 416 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8418 (ptp) REVERT: H 17 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7368 (mmtp) REVERT: H 51 GLU cc_start: 0.8336 (tt0) cc_final: 0.8126 (tt0) REVERT: H 53 MET cc_start: 0.9078 (mtp) cc_final: 0.8803 (mtm) REVERT: H 75 MET cc_start: 0.8648 (mtt) cc_final: 0.8284 (mtt) REVERT: L 5 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8499 (t) REVERT: D 38 ASP cc_start: 0.8440 (m-30) cc_final: 0.8173 (m-30) REVERT: D 62 ASN cc_start: 0.9079 (m110) cc_final: 0.8426 (m110) REVERT: D 95 ASP cc_start: 0.8352 (m-30) cc_final: 0.7666 (m-30) REVERT: F 22 SER cc_start: 0.8278 (p) cc_final: 0.8030 (p) REVERT: F 78 ASN cc_start: 0.7820 (t0) cc_final: 0.7224 (t0) outliers start: 53 outliers final: 43 residues processed: 280 average time/residue: 0.3341 time to fit residues: 138.6619 Evaluate side-chains 279 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 234 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 145 optimal weight: 0.0170 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19614 Z= 0.296 Angle : 0.501 7.046 26643 Z= 0.270 Chirality : 0.043 0.228 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.067 17.138 2715 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.49 % Allowed : 10.53 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.27 (0.17), residues: 2397 helix: 1.08 (0.29), residues: 327 sheet: 0.04 (0.17), residues: 864 loop : 0.19 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 533 HIS 0.008 0.001 HIS B 528 PHE 0.020 0.002 PHE C 279 TYR 0.035 0.001 TYR L 48 ARG 0.009 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 236 time to evaluate : 2.257 Fit side-chains REVERT: A 104 GLN cc_start: 0.7075 (tt0) cc_final: 0.6751 (tt0) REVERT: B 644 PHE cc_start: 0.8201 (m-10) cc_final: 0.7937 (m-10) REVERT: C 175 MET cc_start: 0.9349 (mmt) cc_final: 0.8874 (mmt) REVERT: C 416 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8367 (ptp) REVERT: H 17 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7384 (mmtp) REVERT: H 68 GLN cc_start: 0.8144 (pm20) cc_final: 0.7778 (pm20) REVERT: H 75 MET cc_start: 0.8702 (mtt) cc_final: 0.8346 (mtt) REVERT: L 5 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8500 (t) REVERT: D 38 ASP cc_start: 0.8463 (m-30) cc_final: 0.8141 (m-30) REVERT: D 62 ASN cc_start: 0.9097 (m110) cc_final: 0.8478 (m110) REVERT: D 95 ASP cc_start: 0.8387 (m-30) cc_final: 0.7529 (m-30) REVERT: F 22 SER cc_start: 0.8301 (p) cc_final: 0.8020 (p) outliers start: 51 outliers final: 43 residues processed: 275 average time/residue: 0.3350 time to fit residues: 136.4009 Evaluate side-chains 276 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN F 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19614 Z= 0.216 Angle : 0.471 6.591 26643 Z= 0.255 Chirality : 0.042 0.194 2889 Planarity : 0.004 0.041 3477 Dihedral : 3.996 16.105 2715 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.14 % Allowed : 11.16 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.36 (0.17), residues: 2397 helix: 1.15 (0.29), residues: 327 sheet: 0.20 (0.17), residues: 846 loop : 0.15 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 533 HIS 0.007 0.001 HIS B 528 PHE 0.017 0.001 PHE C 279 TYR 0.028 0.001 TYR L 48 ARG 0.009 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 2.197 Fit side-chains REVERT: A 104 GLN cc_start: 0.7091 (tt0) cc_final: 0.6768 (tt0) REVERT: B 644 PHE cc_start: 0.8186 (m-10) cc_final: 0.7923 (m-10) REVERT: C 175 MET cc_start: 0.9380 (mmt) cc_final: 0.8941 (mmt) REVERT: C 210 MET cc_start: 0.9304 (ttt) cc_final: 0.8862 (ttt) REVERT: C 416 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8433 (ptp) REVERT: H 17 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7375 (mmtp) REVERT: H 68 GLN cc_start: 0.8145 (pm20) cc_final: 0.7788 (pm20) REVERT: H 75 MET cc_start: 0.8686 (mtt) cc_final: 0.8313 (mtt) REVERT: L 5 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (t) REVERT: D 38 ASP cc_start: 0.8447 (m-30) cc_final: 0.8107 (m-30) REVERT: D 62 ASN cc_start: 0.9077 (m110) cc_final: 0.8426 (m110) REVERT: F 22 SER cc_start: 0.8284 (p) cc_final: 0.7994 (p) outliers start: 44 outliers final: 41 residues processed: 271 average time/residue: 0.3418 time to fit residues: 136.7641 Evaluate side-chains 276 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 32 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 156 optimal weight: 0.5980 chunk 236 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19614 Z= 0.281 Angle : 0.494 6.573 26643 Z= 0.267 Chirality : 0.043 0.211 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.047 16.360 2715 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.34 % Allowed : 11.16 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.31 (0.17), residues: 2397 helix: 1.12 (0.29), residues: 327 sheet: 0.15 (0.17), residues: 861 loop : 0.13 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 52 HIS 0.008 0.001 HIS F 32 PHE 0.020 0.002 PHE C 279 TYR 0.034 0.001 TYR G 48 ARG 0.009 0.000 ARG B 556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 231 time to evaluate : 2.440 Fit side-chains REVERT: A 104 GLN cc_start: 0.7110 (tt0) cc_final: 0.6787 (tt0) REVERT: B 578 GLN cc_start: 0.7551 (tp40) cc_final: 0.7042 (tp40) REVERT: B 644 PHE cc_start: 0.8198 (m-10) cc_final: 0.7934 (m-10) REVERT: C 175 MET cc_start: 0.9356 (mmt) cc_final: 0.8903 (mmt) REVERT: C 210 MET cc_start: 0.9311 (ttt) cc_final: 0.8862 (ttt) REVERT: C 416 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8424 (ptp) REVERT: H 17 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7378 (mmtp) REVERT: H 68 GLN cc_start: 0.8139 (pm20) cc_final: 0.7791 (pm20) REVERT: H 75 MET cc_start: 0.8708 (mtt) cc_final: 0.8339 (mtt) REVERT: L 5 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8615 (t) REVERT: D 38 ASP cc_start: 0.8461 (m-30) cc_final: 0.8141 (m-30) REVERT: D 62 ASN cc_start: 0.9094 (m110) cc_final: 0.8474 (m110) REVERT: F 22 SER cc_start: 0.8305 (p) cc_final: 0.8007 (p) outliers start: 48 outliers final: 43 residues processed: 271 average time/residue: 0.3432 time to fit residues: 138.1054 Evaluate side-chains 276 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 32 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN D 32 HIS F 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.102477 restraints weight = 23839.963| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.33 r_work: 0.2892 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19614 Z= 0.223 Angle : 0.475 6.383 26643 Z= 0.257 Chirality : 0.042 0.192 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.006 16.075 2715 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.34 % Allowed : 11.31 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.35 (0.17), residues: 2397 helix: 1.16 (0.29), residues: 327 sheet: 0.20 (0.17), residues: 846 loop : 0.14 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 52 HIS 0.007 0.001 HIS B 528 PHE 0.017 0.001 PHE C 279 TYR 0.030 0.001 TYR G 48 ARG 0.009 0.000 ARG B 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4297.42 seconds wall clock time: 77 minutes 12.37 seconds (4632.37 seconds total)