Starting phenix.real_space_refine (version: dev) on Mon Feb 20 20:08:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/02_2023/7sim_25144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/02_2023/7sim_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_25144/02_2023/7sim_25144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/02_2023/7sim_25144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/02_2023/7sim_25144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/02_2023/7sim_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 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-4877/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: {'CIS': 1, 'PTRANS': 30, '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: {'CIS': 1, 'PTRANS': 30, '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: {' CA': 4, 'CLR': 5, 'NAG': 1, 'PO4': 1, 'TCR': 1} 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: {' CA': 4, 'CLR': 3, 'NAG': 1, 'PO4': 1, 'TCR': 1} 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: 7.71, 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: 5.64 Conformation dependent library (CDL) restraints added in 1.8 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: 1.73 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: 4.35 Time building geometry restraints manager: 5.97 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: 0.210 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: 2.380 Check model and map are aligned: 0.200 Process input model: 36.340 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.260 ------------------------------------------------------------------------------- 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 : 7.90 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 : 1.502 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 1.3345 time to fit residues: 316.8625 Evaluate side-chains 204 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0900 ------------------------------------------------------------------------------- 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: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.7156 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 13156 Z= 0.144 Angle : 0.486 7.880 17900 Z= 0.253 Chirality : 0.040 0.146 2044 Planarity : 0.003 0.040 2204 Dihedral : 5.066 54.014 1806 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 0.88 % 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: 0.66 (0.21), residues: 1546 helix: 1.32 (0.18), residues: 728 sheet: -0.41 (0.39), residues: 184 loop : -0.23 (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 221 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 1.402 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 211 average time/residue: 1.2351 time to fit residues: 285.3470 Evaluate side-chains 209 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 0.1973 time to fit residues: 3.7598 ------------------------------------------------------------------------------- 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: 9.9990 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 312 HIS B 357 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 13156 Z= 0.259 Angle : 0.530 8.589 17900 Z= 0.277 Chirality : 0.042 0.157 2044 Planarity : 0.004 0.051 2204 Dihedral : 5.205 55.894 1806 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 1.33 % 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: 0.71 (0.21), residues: 1546 helix: 1.43 (0.18), residues: 714 sheet: -0.61 (0.36), residues: 212 loop : -0.14 (0.25), residues: 620 *********************** 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: 18 poor density : 205 time to evaluate : 1.520 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 207 average time/residue: 1.2262 time to fit residues: 277.4894 Evaluate side-chains 210 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 2 residues processed: 9 average time/residue: 0.1736 time to fit residues: 4.4926 ------------------------------------------------------------------------------- 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: 4.9990 chunk 106 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 312 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS B 357 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 13156 Z= 0.280 Angle : 0.543 10.377 17900 Z= 0.283 Chirality : 0.043 0.167 2044 Planarity : 0.004 0.053 2204 Dihedral : 5.332 56.616 1806 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 1.62 % 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: 0.59 (0.21), residues: 1546 helix: 1.33 (0.18), residues: 712 sheet: -0.65 (0.36), residues: 212 loop : -0.21 (0.25), residues: 622 *********************** 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 226 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 1.482 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 207 average time/residue: 1.2414 time to fit residues: 281.0976 Evaluate side-chains 215 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 2 residues processed: 9 average time/residue: 0.1842 time to fit residues: 4.7056 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 135 optimal weight: 0.0070 chunk 38 optimal weight: 9.9990 overall best weight: 3.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS A 722 ASN B 179 GLN B 357 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 13156 Z= 0.290 Angle : 0.551 12.267 17900 Z= 0.288 Chirality : 0.043 0.164 2044 Planarity : 0.004 0.048 2204 Dihedral : 5.912 101.337 1806 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 1.92 % 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: 0.51 (0.21), residues: 1546 helix: 1.28 (0.18), residues: 712 sheet: -0.69 (0.36), residues: 212 loop : -0.27 (0.25), residues: 622 *********************** 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 228 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 1.346 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 209 average time/residue: 1.2487 time to fit residues: 285.3689 Evaluate side-chains 212 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 3 residues processed: 8 average time/residue: 0.3523 time to fit residues: 5.5093 ------------------------------------------------------------------------------- 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: 0.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 312 HIS A 338 HIS ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 13156 Z= 0.162 Angle : 0.493 11.625 17900 Z= 0.253 Chirality : 0.040 0.169 2044 Planarity : 0.003 0.042 2204 Dihedral : 5.598 105.684 1806 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 0.75 (0.21), residues: 1546 helix: 1.50 (0.19), residues: 708 sheet: -0.59 (0.36), residues: 212 loop : -0.15 (0.25), residues: 626 *********************** 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 218 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 1.485 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 208 average time/residue: 1.1975 time to fit residues: 273.0299 Evaluate side-chains 207 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1918 time to fit residues: 3.2246 ------------------------------------------------------------------------------- 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: 20.0000 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 338 HIS A 493 ASN A 595 HIS B 176 ASN B 357 ASN B 359 HIS B 493 ASN B 722 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.134 13156 Z= 0.507 Angle : 0.659 13.968 17900 Z= 0.346 Chirality : 0.049 0.202 2044 Planarity : 0.005 0.065 2204 Dihedral : 6.158 107.556 1806 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 2.21 % 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: 1.13 (0.18), residues: 694 sheet: -0.93 (0.34), residues: 216 loop : -0.43 (0.24), residues: 636 *********************** 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 234 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 1.564 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 217 average time/residue: 1.2138 time to fit residues: 288.9246 Evaluate side-chains 220 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 1.513 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.3847 time to fit residues: 6.5201 ------------------------------------------------------------------------------- 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: 4.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 0.0170 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS A 722 ASN B 357 ASN B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 13156 Z= 0.169 Angle : 0.516 12.033 17900 Z= 0.266 Chirality : 0.040 0.158 2044 Planarity : 0.003 0.041 2204 Dihedral : 5.675 107.926 1806 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 1.33 % 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: 0.55 (0.21), residues: 1546 helix: 1.36 (0.19), residues: 706 sheet: -0.65 (0.36), residues: 212 loop : -0.29 (0.25), residues: 628 *********************** 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: 18 poor density : 202 time to evaluate : 1.577 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 213 average time/residue: 1.2544 time to fit residues: 292.8644 Evaluate side-chains 208 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.6454 time to fit residues: 4.2832 ------------------------------------------------------------------------------- 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: 0.9980 chunk 140 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS B 357 ASN B 722 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.124 13156 Z= 0.451 Angle : 0.641 16.110 17900 Z= 0.334 Chirality : 0.047 0.277 2044 Planarity : 0.005 0.068 2204 Dihedral : 6.012 96.466 1806 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.26 (0.21), residues: 1546 helix: 1.16 (0.18), residues: 694 sheet: -0.95 (0.33), residues: 226 loop : -0.39 (0.25), residues: 626 *********************** 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 222 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.516 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 213 average time/residue: 1.2328 time to fit residues: 287.5094 Evaluate side-chains 213 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.1856 time to fit residues: 3.3503 ------------------------------------------------------------------------------- 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: 5.9990 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS A 722 ASN B 357 ASN B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 13156 Z= 0.267 Angle : 0.554 12.765 17900 Z= 0.289 Chirality : 0.042 0.212 2044 Planarity : 0.004 0.054 2204 Dihedral : 5.835 98.024 1806 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.25 % 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: 0.37 (0.21), residues: 1546 helix: 1.26 (0.18), residues: 702 sheet: -0.77 (0.36), residues: 212 loop : -0.44 (0.24), residues: 632 ********************** 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 219 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 1.434 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 211 average time/residue: 1.2533 time to fit residues: 289.1713 Evaluate side-chains 215 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.4698 time to fit residues: 4.9185 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 0.0070 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4164 r_free = 0.4164 target = 0.180563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156793 restraints weight = 17226.989| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.71 r_work: 0.3587 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 13156 Z= 0.186 Angle : 0.506 9.999 17900 Z= 0.264 Chirality : 0.040 0.156 2044 Planarity : 0.003 0.044 2204 Dihedral : 5.569 99.030 1806 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.88 % 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: 0.58 (0.21), residues: 1546 helix: 1.43 (0.19), residues: 702 sheet: -0.68 (0.36), residues: 212 loop : -0.32 (0.25), residues: 632 =============================================================================== Job complete usr+sys time: 4927.36 seconds wall clock time: 88 minutes 0.17 seconds (5280.17 seconds total)