Starting phenix.real_space_refine on Sat Oct 11 09:27:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4k_41034/10_2025/8t4k_41034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4k_41034/10_2025/8t4k_41034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4k_41034/10_2025/8t4k_41034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4k_41034/10_2025/8t4k_41034.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4k_41034/10_2025/8t4k_41034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4k_41034/10_2025/8t4k_41034.cif" } resolution = 2.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8562 2.51 5 N 2310 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13560 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3396 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain breaks: 5 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "G" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Restraints were copied for chains: C, D, E, F, H, I Time building chain proxies: 3.35, per 1000 atoms: 0.25 Number of scatterers: 13560 At special positions: 0 Unit cell: (121.027, 123.431, 116.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2583 8.00 N 2310 7.00 C 8562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 386 " " NAG A 611 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 276 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 301 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 386 " " NAG C 611 " - " ASN C 448 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 197 " " NAG D 605 " - " ASN D 234 " " NAG D 606 " - " ASN D 276 " " NAG D 607 " - " ASN D 295 " " NAG D 608 " - " ASN D 301 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 386 " " NAG D 611 " - " ASN D 448 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN C 262 " " NAG I 1 " - " ASN D 262 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 664.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 21 sheets defined 28.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.048A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.529A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.048A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.530A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.049A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.529A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.567A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.567A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN C 301 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.566A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN D 301 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 315 through 323A current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 459 hydrogen bonds defined for protein. 1251 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: 2.39 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4293 1.35 - 1.47: 3440 1.47 - 1.60: 5959 1.60 - 1.72: 0 1.72 - 1.85: 144 Bond restraints: 13836 Sorted by residual: bond pdb=" N GLU C 269 " pdb=" CA GLU C 269 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.29e-02 6.01e+03 9.97e+00 bond pdb=" N VAL D 270 " pdb=" CA VAL D 270 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" N VAL C 270 " pdb=" CA VAL C 270 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.30e-02 5.92e+03 9.89e+00 bond pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.30e-02 5.92e+03 9.77e+00 bond pdb=" N GLU A 269 " pdb=" CA GLU A 269 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.65e+00 ... (remaining 13831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 16825 1.71 - 3.43: 1625 3.43 - 5.14: 249 5.14 - 6.85: 48 6.85 - 8.56: 12 Bond angle restraints: 18759 Sorted by residual: angle pdb=" CA PRO A 240 " pdb=" N PRO A 240 " pdb=" CD PRO A 240 " ideal model delta sigma weight residual 112.00 104.41 7.59 1.40e+00 5.10e-01 2.94e+01 angle pdb=" CA PRO D 240 " pdb=" N PRO D 240 " pdb=" CD PRO D 240 " ideal model delta sigma weight residual 112.00 104.43 7.57 1.40e+00 5.10e-01 2.93e+01 angle pdb=" CA PRO C 240 " pdb=" N PRO C 240 " pdb=" CD PRO C 240 " ideal model delta sigma weight residual 112.00 104.45 7.55 1.40e+00 5.10e-01 2.91e+01 angle pdb=" N GLN D 246 " pdb=" CA GLN D 246 " pdb=" C GLN D 246 " ideal model delta sigma weight residual 113.88 107.48 6.40 1.23e+00 6.61e-01 2.71e+01 angle pdb=" N GLN A 246 " pdb=" CA GLN A 246 " pdb=" C GLN A 246 " ideal model delta sigma weight residual 113.88 107.50 6.38 1.23e+00 6.61e-01 2.69e+01 ... (remaining 18754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 8217 17.71 - 35.42: 405 35.42 - 53.13: 153 53.13 - 70.84: 42 70.84 - 88.56: 24 Dihedral angle restraints: 8841 sinusoidal: 4107 harmonic: 4734 Sorted by residual: dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.22 50.22 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.20 50.20 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.19 50.19 1 1.00e+01 1.00e-02 3.45e+01 ... (remaining 8838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1960 0.108 - 0.216: 254 0.216 - 0.323: 3 0.323 - 0.431: 0 0.431 - 0.539: 3 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CB ILE F 595 " pdb=" CA ILE F 595 " pdb=" CG1 ILE F 595 " pdb=" CG2 ILE F 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" CB ILE E 595 " pdb=" CA ILE E 595 " pdb=" CG1 ILE E 595 " pdb=" CG2 ILE E 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" CB ILE B 595 " pdb=" CA ILE B 595 " pdb=" CG1 ILE B 595 " pdb=" CG2 ILE B 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 2217 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 639 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C THR F 639 " -0.074 2.00e-02 2.50e+03 pdb=" O THR F 639 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN F 640 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 639 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C THR E 639 " 0.073 2.00e-02 2.50e+03 pdb=" O THR E 639 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN E 640 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 639 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C THR B 639 " 0.073 2.00e-02 2.50e+03 pdb=" O THR B 639 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN B 640 " -0.025 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 9 2.00 - 2.73: 780 2.73 - 3.45: 17621 3.45 - 4.18: 35084 4.18 - 4.90: 58772 Nonbonded interactions: 112266 Sorted by model distance: nonbonded pdb=" NZ LYS B 655 " pdb=" SD MET E 535 " model vdw 1.281 3.480 nonbonded pdb=" NZ LYS E 655 " pdb=" SD MET F 535 " model vdw 1.281 3.480 nonbonded pdb=" SD MET B 535 " pdb=" NZ LYS F 655 " model vdw 1.282 3.480 nonbonded pdb=" CE LYS B 655 " pdb=" SD MET E 535 " model vdw 1.447 3.800 nonbonded pdb=" SD MET B 535 " pdb=" CE LYS F 655 " model vdw 1.447 3.800 ... (remaining 112261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.007 0.084 13908 Z= 0.327 Angle : 1.124 8.565 18942 Z= 0.636 Chirality : 0.067 0.539 2220 Planarity : 0.008 0.078 2316 Dihedral : 13.194 88.556 5670 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.87 % Rotamer: Outliers : 0.62 % Allowed : 7.22 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.20), residues: 1590 helix: 0.19 (0.24), residues: 414 sheet: 0.72 (0.22), residues: 462 loop : 1.14 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 166 TYR 0.012 0.003 TYR E 643 PHE 0.022 0.003 PHE A 383 TRP 0.028 0.004 TRP C 479 HIS 0.033 0.004 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00717 (13836) covalent geometry : angle 1.09735 (18759) SS BOND : bond 0.00580 ( 33) SS BOND : angle 2.25159 ( 66) hydrogen bonds : bond 0.15784 ( 459) hydrogen bonds : angle 7.48111 ( 1251) link_BETA1-4 : bond 0.00228 ( 3) link_BETA1-4 : angle 2.97889 ( 9) link_NAG-ASN : bond 0.00261 ( 36) link_NAG-ASN : angle 2.90803 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.9001 (mmp) cc_final: 0.8733 (mpp) REVERT: B 588 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7665 (ttp-110) REVERT: C 325 HIS cc_start: 0.7525 (m90) cc_final: 0.7130 (m90) REVERT: C 419 TRP cc_start: 0.8225 (m-90) cc_final: 0.7796 (m100) REVERT: E 588 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.7441 (ttp-110) REVERT: D 166 ARG cc_start: 0.8043 (ttp80) cc_final: 0.6570 (mmt90) REVERT: D 327 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7224 (mmt180) REVERT: F 588 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7706 (ttp-110) outliers start: 9 outliers final: 0 residues processed: 219 average time/residue: 0.7028 time to fit residues: 165.9362 Evaluate side-chains 189 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 591 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 352 HIS E 591 GLN D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.153051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124784 restraints weight = 13786.829| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.64 r_work: 0.3244 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13908 Z= 0.166 Angle : 0.637 10.582 18942 Z= 0.334 Chirality : 0.048 0.167 2220 Planarity : 0.004 0.040 2316 Dihedral : 5.096 26.165 2553 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.41 % Allowed : 8.25 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.21), residues: 1590 helix: 1.50 (0.27), residues: 417 sheet: 0.89 (0.23), residues: 444 loop : 0.73 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.016 0.002 TYR A 217 PHE 0.013 0.002 PHE C 320 TRP 0.020 0.002 TRP C 479 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00384 (13836) covalent geometry : angle 0.60949 (18759) SS BOND : bond 0.00550 ( 33) SS BOND : angle 1.61794 ( 66) hydrogen bonds : bond 0.06147 ( 459) hydrogen bonds : angle 5.24510 ( 1251) link_BETA1-4 : bond 0.00127 ( 3) link_BETA1-4 : angle 1.54191 ( 9) link_NAG-ASN : bond 0.00211 ( 36) link_NAG-ASN : angle 2.21358 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7558 (mmt90) REVERT: B 661 LEU cc_start: 0.6855 (mt) cc_final: 0.6556 (mp) REVERT: C 166 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: C 325 HIS cc_start: 0.7992 (m90) cc_final: 0.7608 (m90) REVERT: C 347 LYS cc_start: 0.7583 (pttp) cc_final: 0.7256 (pptt) REVERT: C 500 ARG cc_start: 0.7938 (mmt180) cc_final: 0.7501 (mmt90) REVERT: D 500 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7340 (mmt90) REVERT: F 601 LYS cc_start: 0.7323 (mptt) cc_final: 0.7095 (mtmt) REVERT: F 633 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6401 (mtpt) outliers start: 35 outliers final: 15 residues processed: 215 average time/residue: 0.6381 time to fit residues: 149.1216 Evaluate side-chains 203 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 591 GLN C 352 HIS E 591 GLN E 640 GLN D 352 HIS F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118543 restraints weight = 14064.623| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.68 r_work: 0.3163 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 13908 Z= 0.190 Angle : 0.648 12.449 18942 Z= 0.331 Chirality : 0.048 0.177 2220 Planarity : 0.004 0.035 2316 Dihedral : 5.285 23.574 2553 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.89 % Allowed : 9.35 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.21), residues: 1590 helix: 1.55 (0.27), residues: 420 sheet: 0.80 (0.22), residues: 450 loop : 0.44 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 542 TYR 0.012 0.002 TYR A 217 PHE 0.014 0.002 PHE C 383 TRP 0.017 0.002 TRP C 479 HIS 0.003 0.001 HIS D 352 Details of bonding type rmsd covalent geometry : bond 0.00459 (13836) covalent geometry : angle 0.61728 (18759) SS BOND : bond 0.00599 ( 33) SS BOND : angle 1.80212 ( 66) hydrogen bonds : bond 0.05799 ( 459) hydrogen bonds : angle 5.10213 ( 1251) link_BETA1-4 : bond 0.00099 ( 3) link_BETA1-4 : angle 1.63082 ( 9) link_NAG-ASN : bond 0.00267 ( 36) link_NAG-ASN : angle 2.29673 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8706 (tpt) REVERT: A 500 ARG cc_start: 0.8015 (mmt180) cc_final: 0.7512 (mtt-85) REVERT: C 166 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8268 (ttp80) REVERT: C 347 LYS cc_start: 0.7726 (pttp) cc_final: 0.7430 (pptt) REVERT: C 500 ARG cc_start: 0.7931 (mmt180) cc_final: 0.7572 (mtt-85) REVERT: E 633 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6255 (mtpt) REVERT: D 500 ARG cc_start: 0.7906 (mmt180) cc_final: 0.7402 (mtt-85) REVERT: F 633 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6424 (mtpt) outliers start: 42 outliers final: 13 residues processed: 210 average time/residue: 0.7203 time to fit residues: 163.4434 Evaluate side-chains 193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 640 GLN ** E 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN F 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116693 restraints weight = 14093.681| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.69 r_work: 0.3134 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13908 Z= 0.227 Angle : 0.697 16.237 18942 Z= 0.351 Chirality : 0.049 0.174 2220 Planarity : 0.005 0.041 2316 Dihedral : 5.566 25.499 2553 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.37 % Allowed : 9.14 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.20), residues: 1590 helix: 1.39 (0.27), residues: 420 sheet: 0.97 (0.24), residues: 396 loop : 0.16 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 166 TYR 0.014 0.002 TYR A 217 PHE 0.014 0.002 PHE C 383 TRP 0.017 0.002 TRP C 479 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00549 (13836) covalent geometry : angle 0.66569 (18759) SS BOND : bond 0.00652 ( 33) SS BOND : angle 1.83810 ( 66) hydrogen bonds : bond 0.06004 ( 459) hydrogen bonds : angle 5.22056 ( 1251) link_BETA1-4 : bond 0.00146 ( 3) link_BETA1-4 : angle 1.75996 ( 9) link_NAG-ASN : bond 0.00390 ( 36) link_NAG-ASN : angle 2.45400 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7506 (t) cc_final: 0.7140 (t) REVERT: A 268 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6986 (pt0) REVERT: A 328 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8653 (tpt) REVERT: A 500 ARG cc_start: 0.8081 (mmt180) cc_final: 0.7633 (mtt-85) REVERT: B 601 LYS cc_start: 0.7598 (mptt) cc_final: 0.7330 (mtpt) REVERT: B 633 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6411 (mtpt) REVERT: B 661 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6711 (mp) REVERT: C 137 LYS cc_start: 0.7636 (mttt) cc_final: 0.6573 (pmtt) REVERT: C 347 LYS cc_start: 0.7736 (pttp) cc_final: 0.7411 (pptt) REVERT: C 500 ARG cc_start: 0.8004 (mmt180) cc_final: 0.7703 (mtt-85) REVERT: E 535 MET cc_start: 0.8303 (mpt) cc_final: 0.8014 (mmm) REVERT: E 633 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6252 (mtpt) REVERT: E 660 LEU cc_start: 0.7377 (tp) cc_final: 0.7125 (tt) REVERT: D 47 ASP cc_start: 0.8269 (m-30) cc_final: 0.8043 (m-30) REVERT: D 54 CYS cc_start: 0.7453 (t) cc_final: 0.7141 (t) REVERT: D 396 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8135 (mp) REVERT: D 500 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7459 (mmt90) REVERT: F 633 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6467 (mtpt) outliers start: 49 outliers final: 20 residues processed: 213 average time/residue: 0.7099 time to fit residues: 163.0671 Evaluate side-chains 205 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 157 optimal weight: 0.0040 chunk 99 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN E 591 GLN D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118713 restraints weight = 14147.515| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.69 r_work: 0.3175 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13908 Z= 0.149 Angle : 0.611 14.768 18942 Z= 0.307 Chirality : 0.046 0.173 2220 Planarity : 0.004 0.035 2316 Dihedral : 5.272 24.712 2553 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.61 % Allowed : 11.07 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.21), residues: 1590 helix: 1.58 (0.27), residues: 420 sheet: 0.97 (0.23), residues: 432 loop : 0.19 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 166 TYR 0.010 0.001 TYR F 638 PHE 0.011 0.001 PHE A 391 TRP 0.016 0.001 TRP C 479 HIS 0.003 0.001 HIS D 352 Details of bonding type rmsd covalent geometry : bond 0.00351 (13836) covalent geometry : angle 0.58074 (18759) SS BOND : bond 0.00564 ( 33) SS BOND : angle 1.69932 ( 66) hydrogen bonds : bond 0.05064 ( 459) hydrogen bonds : angle 4.99015 ( 1251) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 1.54550 ( 9) link_NAG-ASN : bond 0.00176 ( 36) link_NAG-ASN : angle 2.19922 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7314 (t) cc_final: 0.6969 (t) REVERT: A 137 LYS cc_start: 0.7567 (mttt) cc_final: 0.6569 (pmtt) REVERT: A 500 ARG cc_start: 0.8062 (mmt180) cc_final: 0.7562 (mmt90) REVERT: B 633 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6396 (mtpt) REVERT: B 657 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: C 103 GLN cc_start: 0.8342 (mt0) cc_final: 0.7273 (tm-30) REVERT: C 137 LYS cc_start: 0.7613 (mttt) cc_final: 0.6542 (pmtt) REVERT: C 347 LYS cc_start: 0.7695 (pttp) cc_final: 0.7369 (pptt) REVERT: C 500 ARG cc_start: 0.7974 (mmt180) cc_final: 0.7647 (mtt-85) REVERT: E 535 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7996 (mmm) REVERT: E 633 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6254 (mtpt) REVERT: D 54 CYS cc_start: 0.7267 (t) cc_final: 0.6976 (t) REVERT: D 114 GLN cc_start: 0.7745 (mt0) cc_final: 0.7417 (pt0) REVERT: D 166 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8205 (tmm160) REVERT: D 500 ARG cc_start: 0.8006 (mmt180) cc_final: 0.7533 (mmt90) outliers start: 38 outliers final: 16 residues processed: 200 average time/residue: 0.6942 time to fit residues: 149.6720 Evaluate side-chains 190 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.0050 chunk 14 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN E 591 GLN D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118994 restraints weight = 14100.539| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.66 r_work: 0.3178 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13908 Z= 0.149 Angle : 0.605 13.818 18942 Z= 0.302 Chirality : 0.046 0.163 2220 Planarity : 0.004 0.037 2316 Dihedral : 5.174 24.489 2553 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.02 % Allowed : 10.93 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.21), residues: 1590 helix: 1.63 (0.27), residues: 420 sheet: 1.05 (0.23), residues: 426 loop : 0.16 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 588 TYR 0.013 0.001 TYR D 217 PHE 0.010 0.001 PHE D 391 TRP 0.014 0.001 TRP C 479 HIS 0.003 0.001 HIS D 352 Details of bonding type rmsd covalent geometry : bond 0.00354 (13836) covalent geometry : angle 0.57661 (18759) SS BOND : bond 0.00572 ( 33) SS BOND : angle 1.60188 ( 66) hydrogen bonds : bond 0.04955 ( 459) hydrogen bonds : angle 4.90800 ( 1251) link_BETA1-4 : bond 0.00166 ( 3) link_BETA1-4 : angle 1.54444 ( 9) link_NAG-ASN : bond 0.00181 ( 36) link_NAG-ASN : angle 2.15828 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7307 (t) cc_final: 0.7001 (t) REVERT: A 137 LYS cc_start: 0.7547 (mttt) cc_final: 0.6546 (pmtt) REVERT: A 166 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7139 (ttp80) REVERT: A 328 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8621 (tpt) REVERT: A 500 ARG cc_start: 0.8041 (mmt180) cc_final: 0.7548 (mmt90) REVERT: B 633 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6381 (mtpt) REVERT: B 657 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6957 (tp30) REVERT: B 661 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6638 (mp) REVERT: C 103 GLN cc_start: 0.8292 (mt0) cc_final: 0.7251 (tm-30) REVERT: C 114 GLN cc_start: 0.7658 (mt0) cc_final: 0.7407 (pt0) REVERT: C 137 LYS cc_start: 0.7617 (mttt) cc_final: 0.6517 (pmtt) REVERT: C 328 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8528 (tpt) REVERT: C 347 LYS cc_start: 0.7641 (pttp) cc_final: 0.7310 (pptt) REVERT: C 500 ARG cc_start: 0.7982 (mmt180) cc_final: 0.7646 (mtt-85) REVERT: E 535 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7980 (mmm) REVERT: E 657 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: D 54 CYS cc_start: 0.7288 (t) cc_final: 0.7003 (t) REVERT: D 114 GLN cc_start: 0.7744 (mt0) cc_final: 0.7442 (pt0) REVERT: D 166 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8225 (tmm160) REVERT: D 347 LYS cc_start: 0.7630 (pttp) cc_final: 0.7321 (pptt) REVERT: D 500 ARG cc_start: 0.7923 (mmt180) cc_final: 0.7447 (mmt90) REVERT: F 633 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6419 (mtpt) outliers start: 44 outliers final: 20 residues processed: 200 average time/residue: 0.7231 time to fit residues: 156.2860 Evaluate side-chains 201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 657 GLU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 19 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN D 352 HIS F 591 GLN F 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.150203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122055 restraints weight = 14130.073| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.58 r_work: 0.3226 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13908 Z= 0.202 Angle : 0.664 14.685 18942 Z= 0.331 Chirality : 0.048 0.176 2220 Planarity : 0.004 0.038 2316 Dihedral : 5.444 24.286 2553 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.09 % Allowed : 11.07 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.20), residues: 1590 helix: 1.49 (0.26), residues: 420 sheet: 0.92 (0.22), residues: 426 loop : 0.12 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 588 TYR 0.012 0.002 TYR D 217 PHE 0.013 0.002 PHE D 383 TRP 0.015 0.002 TRP C 479 HIS 0.003 0.001 HIS D 352 Details of bonding type rmsd covalent geometry : bond 0.00487 (13836) covalent geometry : angle 0.63292 (18759) SS BOND : bond 0.00667 ( 33) SS BOND : angle 1.77261 ( 66) hydrogen bonds : bond 0.05554 ( 459) hydrogen bonds : angle 5.06355 ( 1251) link_BETA1-4 : bond 0.00040 ( 3) link_BETA1-4 : angle 1.73793 ( 9) link_NAG-ASN : bond 0.00335 ( 36) link_NAG-ASN : angle 2.37204 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8295 (m-30) cc_final: 0.8014 (m-30) REVERT: A 54 CYS cc_start: 0.7500 (t) cc_final: 0.7209 (t) REVERT: A 166 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7088 (ttp80) REVERT: A 328 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8558 (tpt) REVERT: A 500 ARG cc_start: 0.8043 (mmt180) cc_final: 0.7597 (mtt-85) REVERT: B 633 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6470 (mtpt) REVERT: C 114 GLN cc_start: 0.7749 (mt0) cc_final: 0.7515 (pt0) REVERT: C 137 LYS cc_start: 0.7803 (mttt) cc_final: 0.6754 (pmtt) REVERT: C 328 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8474 (tpt) REVERT: C 347 LYS cc_start: 0.7724 (pttp) cc_final: 0.7411 (pptt) REVERT: C 500 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7665 (mtt-85) REVERT: E 535 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8070 (mmm) REVERT: E 657 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: D 54 CYS cc_start: 0.7480 (t) cc_final: 0.7195 (t) REVERT: D 114 GLN cc_start: 0.7783 (mt0) cc_final: 0.7482 (pt0) REVERT: D 166 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8256 (tmm160) REVERT: D 327 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7645 (mmt180) REVERT: D 500 ARG cc_start: 0.7950 (mmt180) cc_final: 0.7500 (mmt90) REVERT: F 633 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6440 (mtpt) REVERT: F 657 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7129 (tp30) outliers start: 45 outliers final: 21 residues processed: 198 average time/residue: 0.7276 time to fit residues: 155.2832 Evaluate side-chains 200 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 657 GLU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 0.1980 chunk 138 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN E 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122847 restraints weight = 14117.535| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.57 r_work: 0.3244 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13908 Z= 0.178 Angle : 0.636 14.094 18942 Z= 0.317 Chirality : 0.047 0.175 2220 Planarity : 0.004 0.038 2316 Dihedral : 5.399 24.899 2553 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.82 % Allowed : 11.62 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.20), residues: 1590 helix: 1.53 (0.27), residues: 420 sheet: 0.91 (0.22), residues: 426 loop : 0.10 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 588 TYR 0.011 0.002 TYR D 217 PHE 0.012 0.002 PHE D 383 TRP 0.015 0.002 TRP C 479 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00426 (13836) covalent geometry : angle 0.60583 (18759) SS BOND : bond 0.00628 ( 33) SS BOND : angle 1.65957 ( 66) hydrogen bonds : bond 0.05265 ( 459) hydrogen bonds : angle 4.99543 ( 1251) link_BETA1-4 : bond 0.00122 ( 3) link_BETA1-4 : angle 1.66220 ( 9) link_NAG-ASN : bond 0.00258 ( 36) link_NAG-ASN : angle 2.29384 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8248 (m-30) cc_final: 0.7976 (m-30) REVERT: A 54 CYS cc_start: 0.7401 (t) cc_final: 0.7108 (t) REVERT: A 166 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7117 (ttp80) REVERT: A 430 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7952 (mp) REVERT: A 466 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 500 ARG cc_start: 0.8060 (mmt180) cc_final: 0.7616 (mtt-85) REVERT: C 114 GLN cc_start: 0.7744 (mt0) cc_final: 0.7527 (pt0) REVERT: C 137 LYS cc_start: 0.7808 (mttt) cc_final: 0.6791 (pmtt) REVERT: C 328 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8504 (tpt) REVERT: C 347 LYS cc_start: 0.7685 (pttp) cc_final: 0.7370 (pptt) REVERT: C 500 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7649 (mtt-85) REVERT: E 535 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: D 54 CYS cc_start: 0.7416 (t) cc_final: 0.7140 (t) REVERT: D 114 GLN cc_start: 0.7816 (mt0) cc_final: 0.7532 (pt0) REVERT: D 166 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8244 (tmm160) REVERT: D 327 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7671 (mmt180) REVERT: D 347 LYS cc_start: 0.7659 (pttp) cc_final: 0.7357 (pptt) REVERT: D 500 ARG cc_start: 0.7906 (mmt180) cc_final: 0.7484 (mmt90) REVERT: F 657 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7151 (tp30) outliers start: 41 outliers final: 21 residues processed: 195 average time/residue: 0.7287 time to fit residues: 153.4952 Evaluate side-chains 198 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 29 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN E 651 ASN F 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120955 restraints weight = 14313.336| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.52 r_work: 0.3216 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13908 Z= 0.286 Angle : 0.770 16.204 18942 Z= 0.381 Chirality : 0.052 0.214 2220 Planarity : 0.005 0.042 2316 Dihedral : 5.903 28.153 2553 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.68 % Allowed : 12.03 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1590 helix: 1.24 (0.26), residues: 417 sheet: 0.82 (0.24), residues: 390 loop : -0.07 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 588 TYR 0.016 0.002 TYR A 384 PHE 0.015 0.002 PHE C 383 TRP 0.017 0.002 TRP C 69 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00694 (13836) covalent geometry : angle 0.73520 (18759) SS BOND : bond 0.00848 ( 33) SS BOND : angle 2.06195 ( 66) hydrogen bonds : bond 0.06391 ( 459) hydrogen bonds : angle 5.33161 ( 1251) link_BETA1-4 : bond 0.00137 ( 3) link_BETA1-4 : angle 1.94738 ( 9) link_NAG-ASN : bond 0.00537 ( 36) link_NAG-ASN : angle 2.66948 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7595 (t) cc_final: 0.7345 (t) REVERT: A 83 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6859 (tm-30) REVERT: A 166 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7064 (ttp80) REVERT: A 466 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 500 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7611 (mtt-85) REVERT: B 601 LYS cc_start: 0.7994 (mtpt) cc_final: 0.7783 (mtpt) REVERT: C 114 GLN cc_start: 0.7748 (mt0) cc_final: 0.7516 (pt0) REVERT: C 137 LYS cc_start: 0.7803 (mttt) cc_final: 0.6786 (pmtt) REVERT: C 347 LYS cc_start: 0.7760 (pttp) cc_final: 0.7452 (pptt) REVERT: C 500 ARG cc_start: 0.8013 (mmt180) cc_final: 0.7695 (mtt-85) REVERT: E 535 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: D 54 CYS cc_start: 0.7502 (t) cc_final: 0.7217 (t) REVERT: D 166 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7655 (ttp80) REVERT: D 327 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7636 (mmt180) REVERT: D 500 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7487 (mmt90) REVERT: F 601 LYS cc_start: 0.7768 (mtmt) cc_final: 0.7529 (mtpt) REVERT: F 633 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6467 (mtpt) REVERT: F 657 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7162 (tp30) outliers start: 39 outliers final: 21 residues processed: 204 average time/residue: 0.6707 time to fit residues: 148.1260 Evaluate side-chains 204 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 19 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN B 591 GLN C 67 ASN E 591 GLN D 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124612 restraints weight = 14149.372| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.60 r_work: 0.3258 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13908 Z= 0.127 Angle : 0.595 12.652 18942 Z= 0.298 Chirality : 0.045 0.175 2220 Planarity : 0.004 0.036 2316 Dihedral : 5.291 25.085 2553 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.72 % Allowed : 13.26 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.20), residues: 1590 helix: 1.65 (0.27), residues: 417 sheet: 0.90 (0.22), residues: 411 loop : 0.03 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 588 TYR 0.010 0.001 TYR A 217 PHE 0.009 0.001 PHE A 391 TRP 0.020 0.001 TRP C 419 HIS 0.002 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00293 (13836) covalent geometry : angle 0.56789 (18759) SS BOND : bond 0.00540 ( 33) SS BOND : angle 1.44960 ( 66) hydrogen bonds : bond 0.04697 ( 459) hydrogen bonds : angle 4.85659 ( 1251) link_BETA1-4 : bond 0.00327 ( 3) link_BETA1-4 : angle 1.36925 ( 9) link_NAG-ASN : bond 0.00112 ( 36) link_NAG-ASN : angle 2.13175 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7416 (t) cc_final: 0.7136 (t) REVERT: A 166 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7084 (ttp80) REVERT: A 328 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8637 (tpt) REVERT: A 500 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7591 (mmt90) REVERT: B 601 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7677 (mtpm) REVERT: C 103 GLN cc_start: 0.8334 (mt0) cc_final: 0.7337 (tm-30) REVERT: C 137 LYS cc_start: 0.7794 (mttt) cc_final: 0.6760 (pmtt) REVERT: C 141 MET cc_start: 0.7786 (ttm) cc_final: 0.7565 (ttt) REVERT: C 347 LYS cc_start: 0.7663 (pttp) cc_final: 0.7342 (pptt) REVERT: C 500 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7596 (mtt-85) REVERT: E 535 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8047 (mmm) REVERT: D 54 CYS cc_start: 0.7316 (t) cc_final: 0.7061 (t) REVERT: D 114 GLN cc_start: 0.7851 (mt0) cc_final: 0.7555 (pt0) REVERT: D 166 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7392 (ttp80) REVERT: D 327 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7601 (mmt180) REVERT: D 347 LYS cc_start: 0.7651 (pttp) cc_final: 0.7358 (pptt) REVERT: D 500 ARG cc_start: 0.7926 (mmt180) cc_final: 0.7516 (mmt90) REVERT: F 588 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7818 (ttp80) REVERT: F 601 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7123 (mptt) REVERT: F 657 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7147 (tp30) outliers start: 25 outliers final: 11 residues processed: 184 average time/residue: 0.7330 time to fit residues: 145.3333 Evaluate side-chains 182 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN E 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122775 restraints weight = 14216.483| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.59 r_work: 0.3240 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13908 Z= 0.195 Angle : 0.664 13.792 18942 Z= 0.330 Chirality : 0.048 0.198 2220 Planarity : 0.004 0.041 2316 Dihedral : 5.460 24.527 2553 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.72 % Allowed : 13.26 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.20), residues: 1590 helix: 1.55 (0.26), residues: 417 sheet: 0.88 (0.22), residues: 426 loop : 0.04 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 588 TYR 0.012 0.002 TYR A 217 PHE 0.013 0.002 PHE D 383 TRP 0.021 0.002 TRP C 419 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00469 (13836) covalent geometry : angle 0.63399 (18759) SS BOND : bond 0.00655 ( 33) SS BOND : angle 1.68094 ( 66) hydrogen bonds : bond 0.05428 ( 459) hydrogen bonds : angle 5.00528 ( 1251) link_BETA1-4 : bond 0.00128 ( 3) link_BETA1-4 : angle 1.71507 ( 9) link_NAG-ASN : bond 0.00300 ( 36) link_NAG-ASN : angle 2.36618 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5442.22 seconds wall clock time: 95 minutes 47.45 seconds (5747.45 seconds total)