Starting phenix.real_space_refine on Thu Mar 21 23:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffv_29068/03_2024/8ffv_29068_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffv_29068/03_2024/8ffv_29068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffv_29068/03_2024/8ffv_29068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffv_29068/03_2024/8ffv_29068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffv_29068/03_2024/8ffv_29068_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffv_29068/03_2024/8ffv_29068_trim_updated.pdb" } resolution = 3.01 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= 0.002 sd= 0.040 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: 8 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 10037 2.51 5 N 2649 2.21 5 O 3054 1.98 5 F 1 1.80 5 H 15804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31631 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10279 Classifications: {'peptide': 630} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 614} Chain breaks: 1 Chain: "B" Number of atoms: 10478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 10478 Classifications: {'peptide': 644} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 627} Chain breaks: 2 Chain: "C" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4235 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 247} Chain: "D" Number of atoms: 6547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 6547 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 393} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'DEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.13, per 1000 atoms: 0.42 Number of scatterers: 31631 At special positions: 0 Unit cell: (143.62, 127.755, 118.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 78 16.00 P 6 15.00 Mg 2 11.99 F 1 9.00 O 3054 8.00 N 2649 7.00 C 10037 6.00 H 15804 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.00 Conformation dependent library (CDL) restraints added in 3.2 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 14 sheets defined 43.9% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 42 through 64 removed outlier: 3.507A pdb=" N GLU A 47 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 49 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 58 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 406 through 429 removed outlier: 3.529A pdb=" N VAL A 417 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.847A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 462 removed outlier: 4.779A pdb=" N LYS A 457 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER A 460 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 506 through 513 removed outlier: 4.946A pdb=" N ARG A 510 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 555 through 577 removed outlier: 3.592A pdb=" N LYS A 565 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 566 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU A 569 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 570 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.778A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 641 through 652 Processing helix chain 'A' and resid 657 through 673 Processing helix chain 'A' and resid 682 through 695 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.563A pdb=" N LYS B 58 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 406 through 429 removed outlier: 3.559A pdb=" N ARG B 413 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 417 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.727A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 462 removed outlier: 5.131A pdb=" N GLU B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 513 removed outlier: 4.981A pdb=" N ARG B 510 " --> pdb=" O PHE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 removed outlier: 4.255A pdb=" N VAL B 530 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 533 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 removed outlier: 3.654A pdb=" N LYS B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 578 Processing helix chain 'B' and resid 610 through 615 Processing helix chain 'B' and resid 622 through 626 Processing helix chain 'B' and resid 641 through 652 Processing helix chain 'B' and resid 657 through 673 Processing helix chain 'B' and resid 681 through 695 removed outlier: 4.459A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 556 through 579 Processing helix chain 'C' and resid 584 through 586 No H-bonds generated for 'chain 'C' and resid 584 through 586' Processing helix chain 'C' and resid 589 through 615 removed outlier: 5.041A pdb=" N MET C 601 " --> pdb=" O GLN C 597 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER C 602 " --> pdb=" O TYR C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 637 through 655 removed outlier: 5.071A pdb=" N LYS C 644 " --> pdb=" O TYR C 640 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N HIS C 645 " --> pdb=" O ASP C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 683 through 705 removed outlier: 4.995A pdb=" N GLU C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 704 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 741 removed outlier: 3.523A pdb=" N ARG C 714 " --> pdb=" O ASN C 711 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 720 " --> pdb=" O GLN C 717 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 723 " --> pdb=" O LYS C 720 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C 725 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN C 731 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 741 " --> pdb=" O GLN C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 765 Proline residue: C 762 - end of helix Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 88 through 95 Processing helix chain 'D' and resid 109 through 111 No H-bonds generated for 'chain 'D' and resid 109 through 111' Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 195 through 198 No H-bonds generated for 'chain 'D' and resid 195 through 198' Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.819A pdb=" N ALA D 207 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 209 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 263 through 282 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.694A pdb=" N LYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D 296 " --> pdb=" O GLN D 292 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 331 Processing helix chain 'D' and resid 335 through 348 Processing helix chain 'D' and resid 353 through 366 removed outlier: 3.561A pdb=" N VAL D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 387 through 410 Processing helix chain 'D' and resid 414 through 423 removed outlier: 3.668A pdb=" N ASN D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 171 through 174 removed outlier: 6.963A pdb=" N HIS A 189 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 148 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 187 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 150 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS A 185 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR A 152 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY A 183 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU A 223 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 368 through 371 removed outlier: 6.943A pdb=" N LEU A 363 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LYS A 362 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 387 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N TYR A 364 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 389 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 540 through 542 Processing sheet with id= D, first strand: chain 'A' and resid 585 through 588 removed outlier: 4.366A pdb=" N LYS A 585 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.935A pdb=" N HIS B 189 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B 148 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 187 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B 150 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 185 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 152 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 183 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 223 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 218 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 368 through 371 removed outlier: 6.958A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LYS B 362 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY B 387 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR B 364 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 389 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 540 through 543 Processing sheet with id= H, first strand: chain 'B' and resid 585 through 588 removed outlier: 3.679A pdb=" N LYS B 585 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 674 through 676 Processing sheet with id= J, first strand: chain 'C' and resid 621 through 624 removed outlier: 6.660A pdb=" N LEU C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 77 through 80 removed outlier: 3.507A pdb=" N GLU D 136 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS D 56 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU D 134 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR D 58 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL D 132 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TRP D 60 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE D 130 " --> pdb=" O TRP D 60 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 59 through 61 removed outlier: 4.207A pdb=" N GLY D 59 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 186 through 191 removed outlier: 6.751A pdb=" N ALA D 173 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU D 249 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU D 175 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU D 247 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR D 177 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR D 245 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 157 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE D 218 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN D 155 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR D 220 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ARG D 153 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 176 through 178 679 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.52 Time building geometry restraints manager: 25.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 15780 1.13 - 1.31: 2927 1.31 - 1.48: 6619 1.48 - 1.66: 6454 1.66 - 1.84: 132 Bond restraints: 31912 Sorted by residual: bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.491 -0.103 1.00e-02 1.00e+04 1.06e+02 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.490 -0.102 1.00e-02 1.00e+04 1.04e+02 bond pdb=" NE1 TRP B 297 " pdb=" HE1 TRP B 297 " ideal model delta sigma weight residual 0.860 1.053 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.506 -0.097 1.00e-02 1.00e+04 9.32e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.505 -0.096 1.00e-02 1.00e+04 9.30e+01 ... (remaining 31907 not shown) Histogram of bond angle deviations from ideal: 75.19 - 90.94: 8 90.94 - 106.69: 1491 106.69 - 122.44: 53748 122.44 - 138.19: 2575 138.19 - 153.95: 4 Bond angle restraints: 57826 Sorted by residual: angle pdb=" C TYR A 528 " pdb=" N CYS A 529 " pdb=" CA CYS A 529 " ideal model delta sigma weight residual 120.44 153.95 -33.51 1.36e+00 5.41e-01 6.07e+02 angle pdb=" C THR B 594 " pdb=" N SER B 595 " pdb=" CA SER B 595 " ideal model delta sigma weight residual 120.49 153.08 -32.59 1.42e+00 4.96e-01 5.27e+02 angle pdb=" C MET B 484 " pdb=" N LYS B 485 " pdb=" CA LYS B 485 " ideal model delta sigma weight residual 120.97 152.91 -31.94 1.82e+00 3.02e-01 3.08e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 122.46 17.41 1.00e+00 1.00e+00 3.03e+02 angle pdb=" C THR B 594 " pdb=" N SER B 595 " pdb=" H SER B 595 " ideal model delta sigma weight residual 124.91 75.19 49.72 3.00e+00 1.11e-01 2.75e+02 ... (remaining 57821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 14210 16.49 - 32.98: 456 32.98 - 49.47: 177 49.47 - 65.96: 88 65.96 - 82.45: 23 Dihedral angle restraints: 14954 sinusoidal: 8337 harmonic: 6617 Sorted by residual: dihedral pdb=" CA ALA B 469 " pdb=" C ALA B 469 " pdb=" N SER B 470 " pdb=" CA SER B 470 " ideal model delta harmonic sigma weight residual -180.00 -149.39 -30.61 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA ASN D 197 " pdb=" C ASN D 197 " pdb=" N LEU D 198 " pdb=" CA LEU D 198 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PHE A 437 " pdb=" C PHE A 437 " pdb=" N TYR A 438 " pdb=" CA TYR A 438 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 14951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 2071 0.144 - 0.289: 316 0.289 - 0.433: 9 0.433 - 0.577: 1 0.577 - 0.721: 1 Chirality restraints: 2398 Sorted by residual: chirality pdb=" C8 DEX C 801 " pdb=" C14 DEX C 801 " pdb=" C7 DEX C 801 " pdb=" C9 DEX C 801 " both_signs ideal model delta sigma weight residual False 2.68 1.96 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CB ILE B 378 " pdb=" CA ILE B 378 " pdb=" CG1 ILE B 378 " pdb=" CG2 ILE B 378 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" CA GLU D 215 " pdb=" N GLU D 215 " pdb=" C GLU D 215 " pdb=" CB GLU D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 2395 not shown) Planarity restraints: 4645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 168 " -0.086 2.00e-02 2.50e+03 1.54e-01 2.37e+02 pdb=" N SER A 169 " 0.265 2.00e-02 2.50e+03 pdb=" CA SER A 169 " -0.072 2.00e-02 2.50e+03 pdb=" H SER A 169 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 578 " -0.084 2.00e-02 2.50e+03 1.53e-01 2.34e+02 pdb=" N LEU A 579 " 0.264 2.00e-02 2.50e+03 pdb=" CA LEU A 579 " -0.068 2.00e-02 2.50e+03 pdb=" H LEU A 579 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 638 " 0.084 2.00e-02 2.50e+03 1.52e-01 2.31e+02 pdb=" N ASP A 639 " -0.263 2.00e-02 2.50e+03 pdb=" CA ASP A 639 " 0.075 2.00e-02 2.50e+03 pdb=" H ASP A 639 " 0.104 2.00e-02 2.50e+03 ... (remaining 4642 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 284 1.86 - 2.55: 29017 2.55 - 3.23: 99370 3.23 - 3.92: 125992 3.92 - 4.60: 198342 Nonbonded interactions: 453005 Sorted by model distance: nonbonded pdb=" H GLY B 168 " pdb=" H SER B 169 " model vdw 1.175 2.100 nonbonded pdb=" H ASP A 639 " pdb=" H HIS A 640 " model vdw 1.181 2.100 nonbonded pdb=" H VAL A 544 " pdb=" H THR A 545 " model vdw 1.199 2.100 nonbonded pdb=" H PHE B 384 " pdb=" H ILE B 385 " model vdw 1.219 2.100 nonbonded pdb=" H GLN B 532 " pdb=" H LEU B 533 " model vdw 1.219 2.100 ... (remaining 453000 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' and (resid 15 through 701 or resid 801 through 802)) } 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: 1.910 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: 0.450 Extract box with map and model: 8.440 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 94.120 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.023 0.156 16108 Z= 1.467 Angle : 1.854 33.507 21701 Z= 1.272 Chirality : 0.098 0.721 2398 Planarity : 0.017 0.148 2767 Dihedral : 11.224 82.452 6313 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.19 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 1928 helix: -0.19 (0.16), residues: 848 sheet: 1.43 (0.31), residues: 282 loop : 1.04 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.010 TRP B 162 HIS 0.012 0.003 HIS C 645 PHE 0.057 0.007 PHE B 337 TYR 0.063 0.008 TYR D 245 ARG 0.009 0.001 ARG A 591 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 349 PHE cc_start: 0.9047 (p90) cc_final: 0.8539 (p90) REVERT: B 359 ASN cc_start: 0.7383 (m-40) cc_final: 0.7133 (p0) REVERT: B 373 ASN cc_start: 0.8187 (m-40) cc_final: 0.7926 (m-40) REVERT: C 593 MET cc_start: 0.9090 (mmp) cc_final: 0.8699 (mmm) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.6712 time to fit residues: 146.7159 Evaluate side-chains 90 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 531 GLN D 104 HIS D 269 GLN D 322 HIS D 329 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16108 Z= 0.373 Angle : 0.724 19.450 21701 Z= 0.414 Chirality : 0.044 0.176 2398 Planarity : 0.005 0.035 2767 Dihedral : 8.307 89.337 2249 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.40 % Allowed : 2.30 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 1928 helix: 0.27 (0.17), residues: 861 sheet: 1.21 (0.30), residues: 275 loop : 0.32 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 600 HIS 0.005 0.001 HIS A 684 PHE 0.026 0.002 PHE C 715 TYR 0.020 0.002 TYR B 309 ARG 0.004 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.9064 (t) cc_final: 0.8716 (p) REVERT: C 593 MET cc_start: 0.9301 (mmp) cc_final: 0.8955 (mmm) REVERT: C 600 TRP cc_start: 0.9246 (p-90) cc_final: 0.8962 (p-90) REVERT: D 20 MET cc_start: 0.1844 (mmp) cc_final: 0.1626 (mmp) outliers start: 7 outliers final: 6 residues processed: 105 average time/residue: 0.5522 time to fit residues: 91.4606 Evaluate side-chains 89 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 173 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 633 HIS D 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 16108 Z= 0.428 Angle : 0.659 19.310 21701 Z= 0.377 Chirality : 0.043 0.154 2398 Planarity : 0.004 0.034 2767 Dihedral : 7.615 89.240 2249 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % Rotamer: Outliers : 0.46 % Allowed : 3.05 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1928 helix: 0.37 (0.17), residues: 832 sheet: 0.82 (0.29), residues: 287 loop : 0.09 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 600 HIS 0.006 0.001 HIS B 684 PHE 0.032 0.002 PHE B 337 TYR 0.019 0.002 TYR B 309 ARG 0.004 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.9084 (t) cc_final: 0.8763 (p) REVERT: C 593 MET cc_start: 0.9343 (mmp) cc_final: 0.8991 (mmm) REVERT: C 666 MET cc_start: 0.9697 (mtm) cc_final: 0.9290 (mtp) REVERT: D 20 MET cc_start: 0.1975 (mmp) cc_final: 0.1770 (mmp) outliers start: 8 outliers final: 8 residues processed: 91 average time/residue: 0.5933 time to fit residues: 84.5422 Evaluate side-chains 86 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16108 Z= 0.240 Angle : 0.565 19.103 21701 Z= 0.320 Chirality : 0.040 0.149 2398 Planarity : 0.003 0.037 2767 Dihedral : 7.201 86.040 2249 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 0.40 % Allowed : 3.22 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.19), residues: 1928 helix: 0.48 (0.18), residues: 841 sheet: 0.73 (0.30), residues: 268 loop : -0.06 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 600 HIS 0.004 0.001 HIS A 684 PHE 0.023 0.001 PHE B 337 TYR 0.014 0.001 TYR A 434 ARG 0.003 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 593 MET cc_start: 0.9372 (mmp) cc_final: 0.8813 (mmm) REVERT: D 20 MET cc_start: 0.1775 (mmp) cc_final: 0.1567 (mmp) REVERT: D 211 MET cc_start: 0.7480 (mmm) cc_final: 0.6529 (mmm) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.5143 time to fit residues: 78.2540 Evaluate side-chains 81 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 50.0000 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 138 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 158 optimal weight: 30.0000 chunk 128 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS D 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16108 Z= 0.343 Angle : 0.584 19.232 21701 Z= 0.330 Chirality : 0.040 0.149 2398 Planarity : 0.004 0.037 2767 Dihedral : 7.239 89.804 2249 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.40 % Allowed : 4.03 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.18 (0.19), residues: 1928 helix: 0.52 (0.18), residues: 839 sheet: 0.48 (0.29), residues: 279 loop : -0.31 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 600 HIS 0.006 0.001 HIS B 684 PHE 0.025 0.002 PHE B 337 TYR 0.015 0.002 TYR A 434 ARG 0.003 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 593 MET cc_start: 0.9405 (mmp) cc_final: 0.9039 (mmm) REVERT: D 211 MET cc_start: 0.7566 (mmm) cc_final: 0.6688 (mmm) outliers start: 7 outliers final: 7 residues processed: 88 average time/residue: 0.5233 time to fit residues: 75.4777 Evaluate side-chains 82 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 715 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 50.0000 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 30.0000 chunk 154 optimal weight: 50.0000 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16108 Z= 0.159 Angle : 0.527 19.145 21701 Z= 0.296 Chirality : 0.039 0.149 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.829 88.907 2249 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.23 % Allowed : 4.08 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.30 (0.19), residues: 1928 helix: 0.69 (0.19), residues: 839 sheet: 0.37 (0.30), residues: 273 loop : -0.25 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 600 HIS 0.019 0.001 HIS B 633 PHE 0.020 0.001 PHE C 715 TYR 0.013 0.001 TYR A 434 ARG 0.002 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 593 MET cc_start: 0.9406 (mmp) cc_final: 0.8845 (mmm) REVERT: C 666 MET cc_start: 0.9680 (mtm) cc_final: 0.9277 (mtp) REVERT: D 211 MET cc_start: 0.7469 (mmm) cc_final: 0.7241 (mmm) outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 0.5418 time to fit residues: 69.2976 Evaluate side-chains 75 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 613 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 156 optimal weight: 50.0000 chunk 103 optimal weight: 0.6980 chunk 185 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16108 Z= 0.228 Angle : 0.527 19.177 21701 Z= 0.297 Chirality : 0.039 0.148 2398 Planarity : 0.003 0.037 2767 Dihedral : 6.758 88.740 2249 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.29 % Allowed : 4.54 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.19), residues: 1928 helix: 0.71 (0.19), residues: 843 sheet: 0.35 (0.30), residues: 271 loop : -0.28 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 600 HIS 0.005 0.001 HIS B 684 PHE 0.025 0.001 PHE C 715 TYR 0.013 0.001 TYR A 434 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 593 MET cc_start: 0.9420 (mmp) cc_final: 0.8860 (mmm) REVERT: D 211 MET cc_start: 0.7452 (mmm) cc_final: 0.6607 (mmm) outliers start: 5 outliers final: 5 residues processed: 81 average time/residue: 0.6298 time to fit residues: 81.5422 Evaluate side-chains 78 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain D residue 48 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 55 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16108 Z= 0.157 Angle : 0.516 19.032 21701 Z= 0.289 Chirality : 0.039 0.151 2398 Planarity : 0.003 0.038 2767 Dihedral : 6.511 87.305 2249 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.29 % Allowed : 4.83 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.33 (0.19), residues: 1928 helix: 0.74 (0.19), residues: 850 sheet: 0.31 (0.30), residues: 271 loop : -0.24 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 600 HIS 0.004 0.001 HIS B 684 PHE 0.021 0.001 PHE C 715 TYR 0.012 0.001 TYR A 434 ARG 0.002 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 593 MET cc_start: 0.9421 (mmp) cc_final: 0.8854 (mmm) REVERT: D 211 MET cc_start: 0.7445 (mmm) cc_final: 0.6609 (mmm) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.4497 time to fit residues: 56.7688 Evaluate side-chains 76 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain D residue 48 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16108 Z= 0.217 Angle : 0.522 19.127 21701 Z= 0.293 Chirality : 0.039 0.148 2398 Planarity : 0.003 0.036 2767 Dihedral : 6.544 88.535 2249 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.29 % Allowed : 4.77 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.33 (0.19), residues: 1928 helix: 0.78 (0.19), residues: 847 sheet: 0.30 (0.31), residues: 271 loop : -0.27 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 600 HIS 0.005 0.001 HIS B 684 PHE 0.020 0.001 PHE C 715 TYR 0.013 0.001 TYR A 434 ARG 0.003 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 211 MET cc_start: 0.7465 (mmm) cc_final: 0.6652 (mmm) outliers start: 5 outliers final: 5 residues processed: 74 average time/residue: 0.5196 time to fit residues: 63.2528 Evaluate side-chains 74 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain D residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 chunk 191 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 152 optimal weight: 50.0000 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16108 Z= 0.276 Angle : 0.549 19.246 21701 Z= 0.307 Chirality : 0.039 0.146 2398 Planarity : 0.003 0.035 2767 Dihedral : 6.762 89.287 2249 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.29 % Allowed : 5.06 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.25 (0.19), residues: 1928 helix: 0.74 (0.19), residues: 847 sheet: 0.33 (0.31), residues: 266 loop : -0.38 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 600 HIS 0.005 0.001 HIS B 684 PHE 0.020 0.001 PHE B 337 TYR 0.014 0.001 TYR A 434 ARG 0.003 0.000 ARG A 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 211 MET cc_start: 0.7492 (mmm) cc_final: 0.6702 (mmm) outliers start: 5 outliers final: 5 residues processed: 74 average time/residue: 0.5280 time to fit residues: 64.6431 Evaluate side-chains 75 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain D residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.103453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060681 restraints weight = 125593.188| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.36 r_work: 0.2945 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16108 Z= 0.159 Angle : 0.509 19.060 21701 Z= 0.284 Chirality : 0.038 0.149 2398 Planarity : 0.003 0.034 2767 Dihedral : 6.440 88.396 2249 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.29 % Allowed : 5.00 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.19), residues: 1928 helix: 0.86 (0.19), residues: 848 sheet: 0.25 (0.31), residues: 273 loop : -0.29 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 600 HIS 0.004 0.001 HIS B 684 PHE 0.020 0.001 PHE C 715 TYR 0.012 0.001 TYR A 434 ARG 0.003 0.000 ARG C 558 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5688.61 seconds wall clock time: 104 minutes 15.20 seconds (6255.20 seconds total)