Starting phenix.real_space_refine (version: dev) on Fri May 13 14:47:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/05_2022/7sim_25144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/05_2022/7sim_25144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/05_2022/7sim_25144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/05_2022/7sim_25144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/05_2022/7sim_25144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/05_2022/7sim_25144_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.052 sd= 0.225 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A ASP 480": "OD1" <-> "OD2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 758": "OD1" <-> "OD2" Residue "A PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 190": "OD1" <-> "OD2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 433": "OD1" <-> "OD2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 12826 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'PTRANS': 30, 'CIS': 1, 'TRANS': 749} Chain breaks: 3 Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'PTRANS': 30, 'CIS': 1, 'TRANS': 749} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 179 Unusual residues: {'PO4': 1, ' CA': 4, 'TCR': 1, 'NAG': 1, 'CLR': 5} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 123 Unusual residues: {'PO4': 1, ' CA': 4, 'TCR': 1, 'NAG': 1, 'CLR': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.70, per 1000 atoms: 0.60 Number of scatterers: 12826 At special positions: 0 Unit cell: (100.43, 97.11, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 70 16.00 P 2 15.00 O 2330 8.00 N 2030 7.00 C 8386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 468 " " NAG B 901 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 2.0 seconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 14 sheets defined 44.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.789A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.873A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 611 through 636 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.759A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 681 through 702 Processing helix chain 'A' and resid 723 through 745 Processing helix chain 'A' and resid 770 through 793 Processing helix chain 'A' and resid 803 through 820 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 831 through 860 removed outlier: 5.353A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.789A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.686A pdb=" N ARG B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.884A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 611 through 636 Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.803A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 681 through 702 Processing helix chain 'B' and resid 723 through 745 Processing helix chain 'B' and resid 770 through 793 Processing helix chain 'B' and resid 803 through 820 Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 831 through 860 removed outlier: 5.286A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.171A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 140 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU A 37 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 142 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.167A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.244A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= E, first strand: chain 'A' and resid 550 through 554 Processing sheet with id= F, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= G, first strand: chain 'A' and resid 602 through 604 Processing sheet with id= H, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.167A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 140 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU B 37 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 142 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.191A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.246A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= L, first strand: chain 'B' and resid 550 through 554 Processing sheet with id= M, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= N, first strand: chain 'B' and resid 602 through 604 529 hydrogen bonds defined for protein. 1557 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: 4.76 Time building geometry restraints manager: 6.13 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: 3944 1.34 - 1.46: 2632 1.46 - 1.58: 6496 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 13156 Sorted by residual: bond pdb=" CG TCR B 902 " pdb=" CD1 TCR B 902 " ideal model delta sigma weight residual 1.364 1.473 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" CG TCR A 902 " pdb=" CD1 TCR A 902 " ideal model delta sigma weight residual 1.364 1.472 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O2 PO4 A 903 " pdb=" P PO4 A 903 " ideal model delta sigma weight residual 1.567 1.502 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O4 PO4 B 903 " pdb=" P PO4 B 903 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O2 PO4 B 903 " pdb=" P PO4 B 903 " ideal model delta sigma weight residual 1.567 1.503 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 13151 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.32: 327 106.32 - 113.24: 7266 113.24 - 120.17: 4568 120.17 - 127.10: 5583 127.10 - 134.02: 156 Bond angle restraints: 17900 Sorted by residual: angle pdb=" CA CYS B 598 " pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " ideal model delta sigma weight residual 114.40 124.06 -9.66 2.30e+00 1.89e-01 1.76e+01 angle pdb=" CA LEU A 690 " pdb=" CB LEU A 690 " pdb=" CG LEU A 690 " ideal model delta sigma weight residual 116.30 130.33 -14.03 3.50e+00 8.16e-02 1.61e+01 angle pdb=" CA CYS A 598 " pdb=" CB CYS A 598 " pdb=" SG CYS A 598 " ideal model delta sigma weight residual 114.40 123.22 -8.82 2.30e+00 1.89e-01 1.47e+01 angle pdb=" N GLY B 219 " pdb=" CA GLY B 219 " pdb=" C GLY B 219 " ideal model delta sigma weight residual 112.49 116.76 -4.27 1.21e+00 6.83e-01 1.25e+01 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 112.49 116.76 -4.27 1.21e+00 6.83e-01 1.24e+01 ... (remaining 17895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 6939 17.52 - 35.03: 574 35.03 - 52.55: 113 52.55 - 70.06: 16 70.06 - 87.58: 12 Dihedral angle restraints: 7654 sinusoidal: 3108 harmonic: 4546 Sorted by residual: dihedral pdb=" CB CYS B 358 " pdb=" SG CYS B 358 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual 93.00 34.39 58.61 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 358 " pdb=" SG CYS A 358 " pdb=" SG CYS A 395 " pdb=" CB CYS A 395 " ideal model delta sinusoidal sigma weight residual 93.00 46.44 46.56 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual -86.00 -126.15 40.15 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 7651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1815 0.071 - 0.142: 198 0.142 - 0.213: 14 0.213 - 0.284: 9 0.284 - 0.355: 8 Chirality restraints: 2044 Sorted by residual: chirality pdb=" C14 CLR B 910 " pdb=" C13 CLR B 910 " pdb=" C15 CLR B 910 " pdb=" C8 CLR B 910 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C14 CLR A 911 " pdb=" C13 CLR A 911 " pdb=" C15 CLR A 911 " pdb=" C8 CLR A 911 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C14 CLR B 908 " pdb=" C13 CLR B 908 " pdb=" C15 CLR B 908 " pdb=" C8 CLR B 908 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2041 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 818 " 0.010 2.00e-02 2.50e+03 1.11e-02 3.07e+00 pdb=" CG TRP A 818 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 818 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 818 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 818 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 818 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 818 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 187 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 188 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 187 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 188 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " 0.024 5.00e-02 4.00e+02 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3869 2.82 - 3.34: 12306 3.34 - 3.86: 22394 3.86 - 4.38: 26456 4.38 - 4.90: 43706 Nonbonded interactions: 108731 Sorted by model distance: nonbonded pdb=" OG SER A 657 " pdb=" O SER A 687 " model vdw 2.302 2.440 nonbonded pdb=" OG SER B 657 " pdb=" O SER B 687 " model vdw 2.313 2.440 nonbonded pdb=" O PHE A 351 " pdb=" OG1 THR A 355 " model vdw 2.317 2.440 nonbonded pdb=" O ILE B 857 " pdb=" N LEU B 861 " model vdw 2.327 2.520 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.328 2.440 ... (remaining 108726 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' and (resid 21 through 861 or resid 901 through 910)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 2 5.49 5 S 70 5.16 5 C 8386 2.51 5 N 2030 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.260 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: 2.260 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 37.220 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 0.109 13156 Z= 0.331 Angle : 0.691 14.030 17900 Z= 0.357 Chirality : 0.052 0.355 2044 Planarity : 0.004 0.043 2204 Dihedral : 13.438 87.577 4660 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 (0.20), residues: 1546 helix: 1.10 (0.18), residues: 728 sheet: -0.65 (0.36), residues: 212 loop : -0.37 (0.24), residues: 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.596 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 1.1726 time to fit residues: 280.1896 Evaluate side-chains 204 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 595 HIS A 722 ASN B 357 ASN B 466 HIS B 722 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 13156 Z= 0.149 Angle : 0.491 7.696 17900 Z= 0.255 Chirality : 0.040 0.149 2044 Planarity : 0.003 0.041 2204 Dihedral : 5.092 53.066 1806 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1546 helix: 1.31 (0.18), residues: 728 sheet: -0.42 (0.39), residues: 184 loop : -0.24 (0.24), residues: 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.414 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 210 average time/residue: 1.1098 time to fit residues: 256.4967 Evaluate side-chains 208 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 2 residues processed: 7 average time/residue: 0.1852 time to fit residues: 4.0175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 357 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 13156 Z= 0.259 Angle : 0.530 8.154 17900 Z= 0.278 Chirality : 0.042 0.158 2044 Planarity : 0.004 0.056 2204 Dihedral : 5.231 56.103 1806 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1546 helix: 1.39 (0.18), residues: 716 sheet: -0.62 (0.36), residues: 212 loop : -0.15 (0.25), residues: 618 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.300 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 206 average time/residue: 1.1448 time to fit residues: 258.9347 Evaluate side-chains 210 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 2 residues processed: 9 average time/residue: 0.1698 time to fit residues: 4.5297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 493 ASN B 357 ASN B 493 ASN B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.108 13156 Z= 0.353 Angle : 0.576 9.135 17900 Z= 0.303 Chirality : 0.045 0.178 2044 Planarity : 0.004 0.066 2204 Dihedral : 5.435 58.497 1806 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.47 (0.21), residues: 1546 helix: 1.26 (0.18), residues: 700 sheet: -0.72 (0.36), residues: 212 loop : -0.27 (0.24), residues: 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.466 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 206 average time/residue: 1.1659 time to fit residues: 263.4465 Evaluate side-chains 211 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 1.450 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 3 residues processed: 9 average time/residue: 0.1899 time to fit residues: 4.7077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 344 HIS B 357 ASN B 722 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.122 13156 Z= 0.450 Angle : 0.628 11.773 17900 Z= 0.333 Chirality : 0.047 0.204 2044 Planarity : 0.005 0.063 2204 Dihedral : 5.711 59.754 1806 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.15 (0.20), residues: 1546 helix: 1.03 (0.18), residues: 696 sheet: -0.94 (0.34), residues: 216 loop : -0.45 (0.24), residues: 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 1.323 Fit side-chains outliers start: 36 outliers final: 19 residues processed: 219 average time/residue: 1.0951 time to fit residues: 264.6325 Evaluate side-chains 222 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 7 residues processed: 12 average time/residue: 0.4938 time to fit residues: 9.1435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 179 GLN B 357 ASN B 359 HIS B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.144 13156 Z= 0.344 Angle : 0.595 13.348 17900 Z= 0.314 Chirality : 0.044 0.180 2044 Planarity : 0.004 0.048 2204 Dihedral : 5.568 56.725 1806 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.23 (0.21), residues: 1546 helix: 1.11 (0.18), residues: 694 sheet: -0.80 (0.35), residues: 212 loop : -0.47 (0.24), residues: 640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.315 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 218 average time/residue: 1.1238 time to fit residues: 269.6350 Evaluate side-chains 213 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.1802 time to fit residues: 3.7808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS A 722 ASN B 357 ASN B 722 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 13156 Z= 0.253 Angle : 0.556 13.654 17900 Z= 0.288 Chirality : 0.042 0.155 2044 Planarity : 0.004 0.043 2204 Dihedral : 5.396 53.836 1806 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 (0.21), residues: 1546 helix: 1.16 (0.18), residues: 706 sheet: -0.78 (0.35), residues: 212 loop : -0.44 (0.25), residues: 628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 1.569 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 217 average time/residue: 1.0898 time to fit residues: 261.0340 Evaluate side-chains 213 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.1783 time to fit residues: 3.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 0.0670 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 338 HIS ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 312 HIS B 357 ASN B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 13156 Z= 0.200 Angle : 0.526 12.821 17900 Z= 0.270 Chirality : 0.041 0.159 2044 Planarity : 0.003 0.041 2204 Dihedral : 5.197 53.880 1806 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.45 (0.21), residues: 1546 helix: 1.37 (0.19), residues: 698 sheet: -0.74 (0.36), residues: 212 loop : -0.45 (0.25), residues: 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.440 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 212 average time/residue: 1.1079 time to fit residues: 258.6234 Evaluate side-chains 213 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 7 average time/residue: 0.5382 time to fit residues: 6.4461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 13156 Z= 0.225 Angle : 0.547 15.794 17900 Z= 0.279 Chirality : 0.042 0.166 2044 Planarity : 0.004 0.040 2204 Dihedral : 5.199 55.269 1806 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.42 (0.21), residues: 1546 helix: 1.34 (0.18), residues: 700 sheet: -0.86 (0.34), residues: 226 loop : -0.39 (0.25), residues: 620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 1.628 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 210 average time/residue: 1.0710 time to fit residues: 249.1978 Evaluate side-chains 206 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 2 average time/residue: 0.1559 time to fit residues: 2.4781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 0.0980 chunk 75 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 13156 Z= 0.359 Angle : 0.603 12.124 17900 Z= 0.313 Chirality : 0.045 0.195 2044 Planarity : 0.004 0.055 2204 Dihedral : 5.498 57.992 1806 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 (0.21), residues: 1546 helix: 1.24 (0.19), residues: 692 sheet: -0.93 (0.34), residues: 226 loop : -0.45 (0.25), residues: 628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.462 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 209 average time/residue: 1.1187 time to fit residues: 257.5331 Evaluate side-chains 211 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 5 average time/residue: 0.1740 time to fit residues: 3.3545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 0.1980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 357 ASN B 722 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.180181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156043 restraints weight = 17191.143| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.71 r_work: 0.3760 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.3714 rms_B_bonded: 2.50 restraints_weight: 0.1250 r_work: 0.3689 rms_B_bonded: 2.67 restraints_weight: 0.0625 r_work: 0.3660 rms_B_bonded: 2.93 restraints_weight: 0.0312 r_work: 0.3626 rms_B_bonded: 3.28 restraints_weight: 0.0156 r_work: 0.3585 rms_B_bonded: 3.75 restraints_weight: 0.0078 r_work: 0.3533 rms_B_bonded: 4.37 restraints_weight: 0.0039 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.411 13156 Z= 0.277 Angle : 0.849 73.845 17900 Z= 0.382 Chirality : 0.041 0.188 2044 Planarity : 0.004 0.069 2204 Dihedral : 5.235 52.117 1806 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.40 (0.21), residues: 1546 helix: 1.35 (0.19), residues: 698 sheet: -0.89 (0.34), residues: 226 loop : -0.42 (0.25), residues: 622 =============================================================================== Job complete usr+sys time: 4178.87 seconds wall clock time: 75 minutes 8.71 seconds (4508.71 seconds total)