Starting phenix.real_space_refine on Thu May 15 20:01:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4k_41034/05_2025/8t4k_41034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4k_41034/05_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_41034/05_2025/8t4k_41034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4k_41034/05_2025/8t4k_41034.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4k_41034/05_2025/8t4k_41034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4k_41034/05_2025/8t4k_41034.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: I, H, E, F, C, D Time building chain proxies: 9.07, per 1000 atoms: 0.67 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.61 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: 3.86 Time building geometry restraints manager: 3.85 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: 0.08 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } 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: 9.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (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 TRP 0.028 0.004 TRP C 479 HIS 0.033 0.004 HIS C 66 PHE 0.022 0.003 PHE A 383 TYR 0.012 0.003 TYR E 643 ARG 0.014 0.002 ARG C 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 36) link_NAG-ASN : angle 2.90803 ( 108) link_BETA1-4 : bond 0.00228 ( 3) link_BETA1-4 : angle 2.97889 ( 9) hydrogen bonds : bond 0.15784 ( 459) hydrogen bonds : angle 7.48111 ( 1251) SS BOND : bond 0.00580 ( 33) SS BOND : angle 2.25159 ( 66) covalent geometry : bond 0.00717 (13836) covalent geometry : angle 1.09735 (18759) *********************** 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 : 1.493 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: 1.4035 time to fit residues: 332.7492 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 : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 607 ASN B 653 GLN C 66 HIS C 352 HIS E 591 GLN ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118403 restraints weight = 13851.296| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.65 r_work: 0.3167 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13908 Z= 0.241 Angle : 0.729 10.804 18942 Z= 0.378 Chirality : 0.051 0.185 2220 Planarity : 0.005 0.047 2316 Dihedral : 5.458 22.837 2553 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.89 % Allowed : 7.97 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1590 helix: 1.35 (0.27), residues: 417 sheet: 0.69 (0.22), residues: 456 loop : 0.64 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 479 HIS 0.008 0.001 HIS C 66 PHE 0.015 0.003 PHE D 383 TYR 0.013 0.002 TYR D 384 ARG 0.005 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 36) link_NAG-ASN : angle 2.45414 ( 108) link_BETA1-4 : bond 0.00233 ( 3) link_BETA1-4 : angle 1.83520 ( 9) hydrogen bonds : bond 0.06967 ( 459) hydrogen bonds : angle 5.39231 ( 1251) SS BOND : bond 0.00842 ( 33) SS BOND : angle 1.92944 ( 66) covalent geometry : bond 0.00578 (13836) covalent geometry : angle 0.69781 (18759) *********************** 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 235 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7644 (mmt90) REVERT: B 633 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6533 (mtpt) REVERT: C 178 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8320 (ptt90) REVERT: C 347 LYS cc_start: 0.7657 (pttp) cc_final: 0.7398 (pptt) REVERT: C 500 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7602 (mmt90) REVERT: E 588 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7827 (ttp-110) REVERT: D 54 CYS cc_start: 0.7343 (t) cc_final: 0.6981 (t) REVERT: D 500 ARG cc_start: 0.7873 (mmt180) cc_final: 0.7361 (mmt90) REVERT: F 601 LYS cc_start: 0.7365 (mptt) cc_final: 0.7164 (mmmm) REVERT: F 633 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6423 (mtpt) outliers start: 42 outliers final: 15 residues processed: 221 average time/residue: 1.3499 time to fit residues: 324.2144 Evaluate side-chains 205 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 178 ARG 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 D residue 68 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 396 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 24 optimal weight: 1.9990 chunk 103 optimal weight: 0.0000 chunk 108 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 352 HIS E 591 GLN E 640 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118567 restraints weight = 14047.027| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.65 r_work: 0.3170 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1869 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= 0.189 Angle : 0.643 12.107 18942 Z= 0.328 Chirality : 0.047 0.171 2220 Planarity : 0.004 0.039 2316 Dihedral : 5.389 23.825 2553 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.30 % Allowed : 9.14 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1590 helix: 1.47 (0.27), residues: 420 sheet: 0.81 (0.22), residues: 456 loop : 0.35 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 479 HIS 0.004 0.001 HIS D 352 PHE 0.013 0.002 PHE D 391 TYR 0.012 0.002 TYR A 217 ARG 0.002 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 36) link_NAG-ASN : angle 2.32194 ( 108) link_BETA1-4 : bond 0.00322 ( 3) link_BETA1-4 : angle 1.64038 ( 9) hydrogen bonds : bond 0.05738 ( 459) hydrogen bonds : angle 5.15352 ( 1251) SS BOND : bond 0.00654 ( 33) SS BOND : angle 1.79333 ( 66) covalent geometry : bond 0.00453 (13836) covalent geometry : angle 0.61117 (18759) *********************** 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: 48 poor density : 181 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7384 (t) cc_final: 0.7020 (t) REVERT: A 268 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.7009 (pt0) REVERT: A 328 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8641 (tpt) REVERT: A 500 ARG cc_start: 0.8020 (mmt180) cc_final: 0.7525 (mtt-85) REVERT: B 633 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6485 (mtpt) REVERT: B 661 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6801 (mp) REVERT: C 54 CYS cc_start: 0.7367 (t) cc_final: 0.6952 (t) REVERT: C 178 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8302 (ptt90) REVERT: C 347 LYS cc_start: 0.7704 (pttp) cc_final: 0.7369 (pptt) REVERT: C 500 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7586 (mtt-85) REVERT: E 535 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7950 (mmm) REVERT: E 588 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7708 (ttp-110) REVERT: D 54 CYS cc_start: 0.7337 (t) cc_final: 0.7006 (t) REVERT: D 268 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: D 500 ARG cc_start: 0.7880 (mmt180) cc_final: 0.7349 (mtt-85) REVERT: F 601 LYS cc_start: 0.7437 (mptt) cc_final: 0.7234 (mtmt) REVERT: F 633 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6424 (mtpt) outliers start: 48 outliers final: 20 residues processed: 210 average time/residue: 1.3860 time to fit residues: 315.4250 Evaluate side-chains 205 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE 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 68 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 215 ILE 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 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 D residue 268 GLU 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 11 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN ** E 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN D 352 HIS F 585 HIS F 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119821 restraints weight = 13924.349| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.71 r_work: 0.3208 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13908 Z= 0.139 Angle : 0.589 13.605 18942 Z= 0.298 Chirality : 0.045 0.160 2220 Planarity : 0.004 0.037 2316 Dihedral : 5.099 24.293 2553 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.16 % Allowed : 10.31 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1590 helix: 1.63 (0.27), residues: 420 sheet: 1.13 (0.23), residues: 432 loop : 0.29 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 479 HIS 0.003 0.001 HIS D 352 PHE 0.011 0.001 PHE A 391 TYR 0.014 0.001 TYR A 217 ARG 0.003 0.000 ARG C 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 36) link_NAG-ASN : angle 2.13263 ( 108) link_BETA1-4 : bond 0.00249 ( 3) link_BETA1-4 : angle 1.47867 ( 9) hydrogen bonds : bond 0.04941 ( 459) hydrogen bonds : angle 4.98117 ( 1251) SS BOND : bond 0.00469 ( 33) SS BOND : angle 1.64037 ( 66) covalent geometry : bond 0.00328 (13836) covalent geometry : angle 0.55966 (18759) *********************** 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: 46 poor density : 181 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7209 (t) cc_final: 0.6862 (t) REVERT: A 328 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8503 (tpt) REVERT: A 430 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7932 (mp) REVERT: A 500 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7556 (mtt-85) REVERT: C 54 CYS cc_start: 0.7194 (t) cc_final: 0.6807 (t) REVERT: C 103 GLN cc_start: 0.8267 (mt0) cc_final: 0.7229 (tm-30) REVERT: C 137 LYS cc_start: 0.7608 (mttt) cc_final: 0.6558 (pmtt) REVERT: C 325 HIS cc_start: 0.7944 (m-70) cc_final: 0.7493 (m170) REVERT: C 347 LYS cc_start: 0.7652 (pttp) cc_final: 0.7355 (pptt) REVERT: C 500 ARG cc_start: 0.7936 (mmt180) cc_final: 0.7616 (mtt-85) REVERT: E 535 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7922 (mmm) REVERT: E 660 LEU cc_start: 0.7292 (tp) cc_final: 0.7091 (tt) REVERT: D 54 CYS cc_start: 0.7192 (t) cc_final: 0.6900 (t) REVERT: D 114 GLN cc_start: 0.7676 (mt0) cc_final: 0.7372 (pt0) REVERT: D 500 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7436 (mmt90) REVERT: F 658 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7074 (tt0) outliers start: 46 outliers final: 18 residues processed: 212 average time/residue: 1.3748 time to fit residues: 315.7230 Evaluate side-chains 198 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET 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 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 211 GLU 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 D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR 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 658 GLN 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 106 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120474 restraints weight = 14123.252| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.72 r_work: 0.3219 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13908 Z= 0.128 Angle : 0.573 13.766 18942 Z= 0.287 Chirality : 0.045 0.156 2220 Planarity : 0.003 0.033 2316 Dihedral : 4.936 24.162 2553 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.37 % Allowed : 10.17 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1590 helix: 1.74 (0.27), residues: 420 sheet: 1.00 (0.23), residues: 444 loop : 0.31 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 479 HIS 0.003 0.001 HIS C 105 PHE 0.009 0.001 PHE D 383 TYR 0.013 0.001 TYR A 217 ARG 0.002 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 36) link_NAG-ASN : angle 2.04215 ( 108) link_BETA1-4 : bond 0.00226 ( 3) link_BETA1-4 : angle 1.43671 ( 9) hydrogen bonds : bond 0.04670 ( 459) hydrogen bonds : angle 4.83470 ( 1251) SS BOND : bond 0.00558 ( 33) SS BOND : angle 1.49721 ( 66) covalent geometry : bond 0.00300 (13836) covalent geometry : angle 0.54635 (18759) *********************** 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 222 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7198 (t) cc_final: 0.6879 (t) REVERT: A 137 LYS cc_start: 0.7565 (mttt) cc_final: 0.6573 (pmtt) REVERT: A 151 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8351 (ttm170) REVERT: A 328 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8519 (tpt) REVERT: A 430 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7870 (mp) REVERT: A 500 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7510 (mmt90) REVERT: B 633 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6487 (mtpt) REVERT: B 657 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6993 (tp30) REVERT: B 660 LEU cc_start: 0.7334 (tp) cc_final: 0.7133 (tt) REVERT: B 661 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6612 (mp) REVERT: C 103 GLN cc_start: 0.8275 (mt0) cc_final: 0.7244 (tm-30) REVERT: C 137 LYS cc_start: 0.7638 (mttt) cc_final: 0.6593 (pmtt) REVERT: C 325 HIS cc_start: 0.7984 (m-70) cc_final: 0.7553 (m170) REVERT: C 347 LYS cc_start: 0.7669 (pttp) cc_final: 0.7321 (pptt) REVERT: C 500 ARG cc_start: 0.7961 (mmt180) cc_final: 0.7641 (mtt-85) REVERT: E 535 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7954 (mmm) REVERT: D 54 CYS cc_start: 0.7149 (t) cc_final: 0.6862 (t) REVERT: D 347 LYS cc_start: 0.7584 (pttp) cc_final: 0.7262 (pptt) REVERT: D 500 ARG cc_start: 0.7931 (mmt180) cc_final: 0.7471 (mmt90) REVERT: F 658 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6971 (tt0) outliers start: 49 outliers final: 20 residues processed: 205 average time/residue: 1.4221 time to fit residues: 316.6752 Evaluate side-chains 197 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE 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 211 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 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR 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 636 SER Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 154 optimal weight: 0.0980 chunk 137 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 F 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119967 restraints weight = 14163.908| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.69 r_work: 0.3199 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13908 Z= 0.136 Angle : 0.585 13.108 18942 Z= 0.292 Chirality : 0.045 0.167 2220 Planarity : 0.004 0.035 2316 Dihedral : 4.925 23.844 2553 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.02 % Allowed : 10.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1590 helix: 1.73 (0.27), residues: 420 sheet: 0.98 (0.23), residues: 438 loop : 0.26 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 479 HIS 0.002 0.001 HIS D 105 PHE 0.010 0.001 PHE A 383 TYR 0.010 0.001 TYR A 217 ARG 0.003 0.000 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 36) link_NAG-ASN : angle 2.06653 ( 108) link_BETA1-4 : bond 0.00205 ( 3) link_BETA1-4 : angle 1.45390 ( 9) hydrogen bonds : bond 0.04723 ( 459) hydrogen bonds : angle 4.83379 ( 1251) SS BOND : bond 0.00555 ( 33) SS BOND : angle 1.51691 ( 66) covalent geometry : bond 0.00321 (13836) covalent geometry : angle 0.55840 (18759) *********************** 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 211 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7206 (t) cc_final: 0.6901 (t) REVERT: A 137 LYS cc_start: 0.7549 (mttt) cc_final: 0.6553 (pmtt) REVERT: A 328 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8571 (tpt) REVERT: A 430 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 500 ARG cc_start: 0.8020 (mmt180) cc_final: 0.7533 (mmt90) REVERT: B 633 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6488 (mtpt) REVERT: B 657 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: C 103 GLN cc_start: 0.8283 (mt0) cc_final: 0.7251 (tm-30) REVERT: C 114 GLN cc_start: 0.7628 (mt0) cc_final: 0.7378 (pt0) REVERT: C 137 LYS cc_start: 0.7620 (mttt) cc_final: 0.6565 (pmtt) REVERT: C 325 HIS cc_start: 0.7919 (m-70) cc_final: 0.7518 (m170) REVERT: C 328 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8580 (tpt) REVERT: C 347 LYS cc_start: 0.7649 (pttp) cc_final: 0.7305 (pptt) REVERT: C 500 ARG cc_start: 0.7979 (mmt180) cc_final: 0.7667 (mtt-85) REVERT: E 535 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7973 (mmm) REVERT: D 54 CYS cc_start: 0.7176 (t) cc_final: 0.6897 (t) REVERT: D 114 GLN cc_start: 0.7722 (mt0) cc_final: 0.7383 (pt0) REVERT: D 166 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7273 (ttp80) REVERT: D 327 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7538 (mmt180) REVERT: D 347 LYS cc_start: 0.7605 (pttp) cc_final: 0.7275 (pptt) REVERT: D 500 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7469 (mmt90) REVERT: F 657 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7158 (tp30) outliers start: 44 outliers final: 18 residues processed: 197 average time/residue: 1.4373 time to fit residues: 305.9513 Evaluate side-chains 193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE 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 211 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 327 ARG 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 636 SER Chi-restraints excluded: chain F residue 657 GLU 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 127 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.0030 chunk 110 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121298 restraints weight = 14076.110| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.65 r_work: 0.3206 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13908 Z= 0.123 Angle : 0.564 11.938 18942 Z= 0.282 Chirality : 0.045 0.169 2220 Planarity : 0.003 0.033 2316 Dihedral : 4.833 23.758 2553 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.68 % Allowed : 11.13 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1590 helix: 1.86 (0.27), residues: 417 sheet: 0.99 (0.23), residues: 438 loop : 0.26 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 479 HIS 0.002 0.001 HIS C 105 PHE 0.009 0.001 PHE D 383 TYR 0.010 0.001 TYR A 217 ARG 0.003 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 36) link_NAG-ASN : angle 2.00089 ( 108) link_BETA1-4 : bond 0.00272 ( 3) link_BETA1-4 : angle 1.39053 ( 9) hydrogen bonds : bond 0.04495 ( 459) hydrogen bonds : angle 4.71865 ( 1251) SS BOND : bond 0.00518 ( 33) SS BOND : angle 1.41278 ( 66) covalent geometry : bond 0.00289 (13836) covalent geometry : angle 0.53867 (18759) *********************** 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 206 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7169 (t) cc_final: 0.6875 (t) REVERT: A 500 ARG cc_start: 0.8019 (mmt180) cc_final: 0.7568 (mtt-85) REVERT: B 633 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6449 (mtpt) REVERT: C 103 GLN cc_start: 0.8294 (mt0) cc_final: 0.7276 (tm-30) REVERT: C 114 GLN cc_start: 0.7626 (mt0) cc_final: 0.7388 (pt0) REVERT: C 137 LYS cc_start: 0.7653 (mttt) cc_final: 0.6566 (pmtt) REVERT: C 325 HIS cc_start: 0.7925 (m-70) cc_final: 0.7531 (m170) REVERT: C 328 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8594 (tpt) REVERT: C 347 LYS cc_start: 0.7653 (pttp) cc_final: 0.7310 (pptt) REVERT: C 500 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7664 (mtt-85) REVERT: E 535 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7954 (mmm) REVERT: D 54 CYS cc_start: 0.7152 (t) cc_final: 0.6877 (t) REVERT: D 114 GLN cc_start: 0.7714 (mt0) cc_final: 0.7386 (pt0) REVERT: D 166 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7273 (ttp80) REVERT: D 327 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7557 (mmt180) REVERT: D 500 ARG cc_start: 0.7946 (mmt180) cc_final: 0.7495 (mmt90) outliers start: 39 outliers final: 19 residues processed: 194 average time/residue: 1.4574 time to fit residues: 305.6918 Evaluate side-chains 189 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 123 THR 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 C residue 75 VAL Chi-restraints excluded: chain C residue 166 ARG 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 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 211 GLU 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 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 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 F 591 GLN F 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.151477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123258 restraints weight = 14176.837| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.60 r_work: 0.3259 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13908 Z= 0.178 Angle : 0.628 13.071 18942 Z= 0.313 Chirality : 0.047 0.181 2220 Planarity : 0.004 0.036 2316 Dihedral : 5.157 23.502 2553 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.61 % Allowed : 11.75 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1590 helix: 1.71 (0.26), residues: 417 sheet: 1.02 (0.23), residues: 426 loop : 0.21 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 69 HIS 0.003 0.001 HIS E 585 PHE 0.012 0.002 PHE C 383 TYR 0.010 0.002 TYR D 384 ARG 0.005 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 36) link_NAG-ASN : angle 2.23618 ( 108) link_BETA1-4 : bond 0.00069 ( 3) link_BETA1-4 : angle 1.65501 ( 9) hydrogen bonds : bond 0.05197 ( 459) hydrogen bonds : angle 4.92725 ( 1251) SS BOND : bond 0.00608 ( 33) SS BOND : angle 1.60678 ( 66) covalent geometry : bond 0.00428 (13836) covalent geometry : angle 0.59938 (18759) *********************** 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 211 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7359 (t) cc_final: 0.7090 (t) REVERT: A 151 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8358 (ttm170) REVERT: A 166 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7059 (ttp80) REVERT: A 500 ARG cc_start: 0.8030 (mmt180) cc_final: 0.7586 (mtt-85) REVERT: B 633 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6441 (mtpt) REVERT: C 103 GLN cc_start: 0.8367 (mt0) cc_final: 0.7368 (tm-30) REVERT: C 114 GLN cc_start: 0.7731 (mt0) cc_final: 0.7514 (pt0) REVERT: C 137 LYS cc_start: 0.7829 (mttt) cc_final: 0.6810 (pmtt) REVERT: C 325 HIS cc_start: 0.7882 (m-70) cc_final: 0.7485 (m170) REVERT: C 328 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8531 (tpt) REVERT: C 347 LYS cc_start: 0.7695 (pttp) cc_final: 0.7364 (pptt) REVERT: C 500 ARG cc_start: 0.7978 (mmt180) cc_final: 0.7668 (mtt-85) REVERT: E 535 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8017 (mmm) REVERT: D 47 ASP cc_start: 0.8223 (m-30) cc_final: 0.7958 (m-30) REVERT: D 54 CYS cc_start: 0.7222 (t) cc_final: 0.6950 (t) REVERT: D 114 GLN cc_start: 0.7759 (mt0) cc_final: 0.7454 (pt0) REVERT: D 166 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8187 (tmm160) REVERT: D 347 LYS cc_start: 0.7642 (pttp) cc_final: 0.7318 (pptt) REVERT: D 500 ARG cc_start: 0.7921 (mmt180) cc_final: 0.7493 (mtt-85) REVERT: F 633 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6442 (mtpt) outliers start: 38 outliers final: 20 residues processed: 194 average time/residue: 1.3683 time to fit residues: 287.4581 Evaluate side-chains 197 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 151 ARG 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 633 LYS Chi-restraints excluded: chain B residue 636 SER 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 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 75 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 145 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 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 F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.150528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122329 restraints weight = 14147.521| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.59 r_work: 0.3244 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13908 Z= 0.200 Angle : 0.663 13.734 18942 Z= 0.331 Chirality : 0.048 0.186 2220 Planarity : 0.004 0.036 2316 Dihedral : 5.373 23.658 2553 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.54 % Allowed : 12.30 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1590 helix: 1.60 (0.26), residues: 417 sheet: 1.00 (0.23), residues: 408 loop : 0.14 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 69 HIS 0.003 0.001 HIS A 249 PHE 0.013 0.002 PHE D 383 TYR 0.011 0.002 TYR A 384 ARG 0.004 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 36) link_NAG-ASN : angle 2.34768 ( 108) link_BETA1-4 : bond 0.00097 ( 3) link_BETA1-4 : angle 1.68234 ( 9) hydrogen bonds : bond 0.05478 ( 459) hydrogen bonds : angle 5.03178 ( 1251) SS BOND : bond 0.00672 ( 33) SS BOND : angle 1.74531 ( 66) covalent geometry : bond 0.00479 (13836) covalent geometry : angle 0.63296 (18759) *********************** 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 210 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7414 (t) cc_final: 0.7146 (t) REVERT: A 151 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8471 (ttm170) REVERT: A 166 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7087 (ttp80) REVERT: A 328 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8543 (tpt) REVERT: A 430 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7960 (mp) REVERT: A 500 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7574 (mtt-85) REVERT: B 633 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6427 (mtpt) REVERT: C 103 GLN cc_start: 0.8356 (mt0) cc_final: 0.7334 (tm-30) REVERT: C 137 LYS cc_start: 0.7808 (mttt) cc_final: 0.6765 (pmtt) REVERT: C 325 HIS cc_start: 0.7913 (m-70) cc_final: 0.7500 (m170) REVERT: C 328 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8489 (tpt) REVERT: C 347 LYS cc_start: 0.7695 (pttp) cc_final: 0.7365 (pptt) REVERT: C 500 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7635 (mtt-85) REVERT: E 535 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: E 588 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7959 (ttp-110) REVERT: D 47 ASP cc_start: 0.8256 (m-30) cc_final: 0.7986 (m-30) REVERT: D 54 CYS cc_start: 0.7390 (t) cc_final: 0.7124 (t) REVERT: D 114 GLN cc_start: 0.7741 (mt0) cc_final: 0.7412 (pt0) REVERT: D 166 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8222 (tmm160) REVERT: D 347 LYS cc_start: 0.7638 (pttp) cc_final: 0.7304 (pptt) REVERT: D 500 ARG cc_start: 0.7888 (mmt180) cc_final: 0.7439 (mtt-85) REVERT: F 588 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7859 (ttp-110) REVERT: F 633 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6384 (mtpt) outliers start: 37 outliers final: 22 residues processed: 193 average time/residue: 1.4347 time to fit residues: 299.4482 Evaluate side-chains 203 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 151 ARG 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 A residue 430 ILE 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 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 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 75 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 47 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122791 restraints weight = 14190.664| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.51 r_work: 0.3260 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2495 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= 0.172 Angle : 0.635 13.127 18942 Z= 0.317 Chirality : 0.047 0.177 2220 Planarity : 0.004 0.036 2316 Dihedral : 5.321 24.218 2553 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.61 % Allowed : 12.30 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1590 helix: 1.65 (0.27), residues: 417 sheet: 0.99 (0.23), residues: 420 loop : 0.12 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 419 HIS 0.002 0.001 HIS C 105 PHE 0.011 0.002 PHE C 383 TYR 0.010 0.001 TYR A 217 ARG 0.004 0.000 ARG B 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 36) link_NAG-ASN : angle 2.26034 ( 108) link_BETA1-4 : bond 0.00164 ( 3) link_BETA1-4 : angle 1.59836 ( 9) hydrogen bonds : bond 0.05195 ( 459) hydrogen bonds : angle 4.95150 ( 1251) SS BOND : bond 0.00619 ( 33) SS BOND : angle 1.63151 ( 66) covalent geometry : bond 0.00409 (13836) covalent geometry : angle 0.60624 (18759) ********************** 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 207 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7370 (t) cc_final: 0.7109 (t) REVERT: A 151 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8326 (ttm170) REVERT: A 166 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7065 (ttp80) REVERT: A 328 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8552 (tpt) REVERT: A 430 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.8007 (mp) REVERT: A 466 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 500 ARG cc_start: 0.8068 (mmt180) cc_final: 0.7593 (mtt-85) REVERT: B 588 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7975 (ttp-110) REVERT: B 601 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7628 (mtpm) REVERT: B 633 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6469 (mtpt) REVERT: C 103 GLN cc_start: 0.8357 (mt0) cc_final: 0.7345 (tm-30) REVERT: C 137 LYS cc_start: 0.7823 (mttt) cc_final: 0.6806 (pmtt) REVERT: C 325 HIS cc_start: 0.7872 (m-70) cc_final: 0.7463 (m170) REVERT: C 328 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8559 (tpt) REVERT: C 347 LYS cc_start: 0.7707 (pttp) cc_final: 0.7383 (pptt) REVERT: C 500 ARG cc_start: 0.7988 (mmt180) cc_final: 0.7663 (mtt-85) REVERT: E 535 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: E 588 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7964 (ttp-110) REVERT: D 47 ASP cc_start: 0.8242 (m-30) cc_final: 0.7979 (m-30) REVERT: D 54 CYS cc_start: 0.7353 (t) cc_final: 0.7096 (t) REVERT: D 114 GLN cc_start: 0.7740 (mt0) cc_final: 0.7458 (pt0) REVERT: D 166 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8220 (tmm160) REVERT: D 327 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7524 (mmt180) REVERT: D 347 LYS cc_start: 0.7641 (pttp) cc_final: 0.7316 (pptt) REVERT: D 500 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7490 (mtt-85) REVERT: F 588 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7789 (ttp80) REVERT: F 633 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6378 (mtpt) outliers start: 38 outliers final: 20 residues processed: 188 average time/residue: 1.4365 time to fit residues: 292.9127 Evaluate side-chains 197 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 151 ARG 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 A residue 430 ILE 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 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG 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 75 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 327 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.151738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124334 restraints weight = 14277.545| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.54 r_work: 0.3265 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13908 Z= 0.136 Angle : 0.590 11.885 18942 Z= 0.295 Chirality : 0.046 0.169 2220 Planarity : 0.004 0.035 2316 Dihedral : 5.104 24.344 2553 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.54 % Allowed : 12.30 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1590 helix: 1.79 (0.27), residues: 417 sheet: 0.94 (0.23), residues: 432 loop : 0.18 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 419 HIS 0.002 0.001 HIS C 105 PHE 0.011 0.001 PHE D 383 TYR 0.010 0.001 TYR A 217 ARG 0.003 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 36) link_NAG-ASN : angle 2.10408 ( 108) link_BETA1-4 : bond 0.00225 ( 3) link_BETA1-4 : angle 1.44047 ( 9) hydrogen bonds : bond 0.04713 ( 459) hydrogen bonds : angle 4.78918 ( 1251) SS BOND : bond 0.00544 ( 33) SS BOND : angle 1.44276 ( 66) covalent geometry : bond 0.00319 (13836) covalent geometry : angle 0.56397 (18759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10824.58 seconds wall clock time: 187 minutes 4.95 seconds (11224.95 seconds total)