Starting phenix.real_space_refine on Fri Jun 6 14:48:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tti_26116/06_2025/7tti_26116_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tti_26116/06_2025/7tti_26116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tti_26116/06_2025/7tti_26116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tti_26116/06_2025/7tti_26116.map" model { file = "/net/cci-nas-00/data/ceres_data/7tti_26116/06_2025/7tti_26116_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tti_26116/06_2025/7tti_26116_trim.cif" } resolution = 3.5 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= 0.000 sd= 0.043 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 62 5.16 5 C 5030 2.51 5 N 1208 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 3753 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 27, 'TRANS': 514} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 3753 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 27, 'TRANS': 514} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'JUX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'JUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.03, per 1000 atoms: 0.66 Number of scatterers: 7670 At special positions: 0 Unit cell: (85.905, 108.675, 104.535, 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 62 16.00 O 1370 8.00 N 1208 7.00 C 5030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG E 1 " - " ASN B 312 " " NAG F 1 " - " ASN B 361 " Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 71.0% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 120 through 134 removed outlier: 4.442A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix removed outlier: 3.522A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLY A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 176 removed outlier: 4.239A pdb=" N TRP A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.587A pdb=" N MET A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.841A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 243 through 268 removed outlier: 3.748A pdb=" N THR A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 301 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 354 through 360 removed outlier: 4.170A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 429 through 432 removed outlier: 3.515A pdb=" N THR A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.577A pdb=" N ARG A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 450 through 477 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.713A pdb=" N ARG A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.030A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.503A pdb=" N THR A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 500' Processing helix chain 'A' and resid 503 through 536 removed outlier: 4.083A pdb=" N ILE A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Proline residue: A 527 - end of helix removed outlier: 3.782A pdb=" N ASP A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 removed outlier: 3.663A pdb=" N ARG A 543 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.858A pdb=" N GLU A 553 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 578 through 602 removed outlier: 3.823A pdb=" N SER A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 656 removed outlier: 4.243A pdb=" N ALA A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 134 removed outlier: 4.428A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix removed outlier: 4.561A pdb=" N GLY B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 176 removed outlier: 4.245A pdb=" N TRP B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.595A pdb=" N MET B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.763A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 243 through 268 removed outlier: 3.734A pdb=" N THR B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 301 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 354 through 360 removed outlier: 4.153A pdb=" N MET B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 429 through 432 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.575A pdb=" N ARG B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 450 through 477 Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.725A pdb=" N ARG B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.028A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.564A pdb=" N LEU B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 536 removed outlier: 4.081A pdb=" N ILE B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Proline residue: B 527 - end of helix removed outlier: 3.763A pdb=" N ASP B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.652A pdb=" N ARG B 543 " --> pdb=" O PRO B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.864A pdb=" N GLU B 553 " --> pdb=" O VAL B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 578 through 602 removed outlier: 3.810A pdb=" N SER B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 656 removed outlier: 4.240A pdb=" N ALA B 617 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 640 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'B' and resid 306 through 310 515 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2346 1.34 - 1.46: 1915 1.46 - 1.58: 3503 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 7852 Sorted by residual: bond pdb=" C5 JUX B1201 " pdb=" S1 JUX B1201 " ideal model delta sigma weight residual 1.734 1.400 0.334 2.00e-02 2.50e+03 2.80e+02 bond pdb=" C5 JUX A1201 " pdb=" S1 JUX A1201 " ideal model delta sigma weight residual 1.734 1.400 0.334 2.00e-02 2.50e+03 2.79e+02 bond pdb=" C8 JUX A1201 " pdb=" S1 JUX A1201 " ideal model delta sigma weight residual 1.721 1.394 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C8 JUX B1201 " pdb=" S1 JUX B1201 " ideal model delta sigma weight residual 1.721 1.394 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C9 JUX A1201 " pdb=" S2 JUX A1201 " ideal model delta sigma weight residual 1.823 1.745 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 7847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 10748 3.13 - 6.26: 42 6.26 - 9.39: 8 9.39 - 12.51: 4 12.51 - 15.64: 2 Bond angle restraints: 10804 Sorted by residual: angle pdb=" C7 JUX A1201 " pdb=" C6 JUX A1201 " pdb=" N2 JUX A1201 " ideal model delta sigma weight residual 119.28 134.92 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C7 JUX B1201 " pdb=" C6 JUX B1201 " pdb=" N2 JUX B1201 " ideal model delta sigma weight residual 119.28 134.81 -15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" N JUX A1201 " pdb=" CA JUX A1201 " pdb=" C JUX A1201 " ideal model delta sigma weight residual 119.72 108.51 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" N JUX B1201 " pdb=" CA JUX B1201 " pdb=" C JUX B1201 " ideal model delta sigma weight residual 119.72 108.96 10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N ILE A 538 " pdb=" CA ILE A 538 " pdb=" C ILE A 538 " ideal model delta sigma weight residual 111.81 108.78 3.03 8.60e-01 1.35e+00 1.24e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.81: 4279 22.81 - 45.61: 277 45.61 - 68.41: 44 68.41 - 91.22: 18 91.22 - 114.02: 8 Dihedral angle restraints: 4626 sinusoidal: 1526 harmonic: 3100 Sorted by residual: dihedral pdb=" CA CYS B 626 " pdb=" C CYS B 626 " pdb=" N LEU B 627 " pdb=" CA LEU B 627 " ideal model delta harmonic sigma weight residual 180.00 146.56 33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA CYS A 626 " pdb=" C CYS A 626 " pdb=" N LEU A 627 " pdb=" CA LEU A 627 " ideal model delta harmonic sigma weight residual 180.00 146.63 33.37 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 323 " pdb=" CB CYS A 323 " ideal model delta sinusoidal sigma weight residual -86.00 -133.74 47.74 1 1.00e+01 1.00e-02 3.14e+01 ... (remaining 4623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1011 0.037 - 0.074: 276 0.074 - 0.111: 77 0.111 - 0.149: 12 0.149 - 0.186: 2 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA CYS B 626 " pdb=" N CYS B 626 " pdb=" C CYS B 626 " pdb=" CB CYS B 626 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA CYS A 626 " pdb=" N CYS A 626 " pdb=" C CYS A 626 " pdb=" CB CYS A 626 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA JUX B1201 " pdb=" N JUX B1201 " pdb=" C JUX B1201 " pdb=" C4 JUX B1201 " both_signs ideal model delta sigma weight residual True 2.30 -2.44 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1375 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N JUX B1201 " 0.122 2.00e-02 2.50e+03 9.89e-02 1.47e+02 pdb=" CA JUX B1201 " -0.138 2.00e-02 2.50e+03 pdb=" OH JUX B1201 " -0.131 2.00e-02 2.50e+03 pdb=" C1 JUX B1201 " 0.038 2.00e-02 2.50e+03 pdb=" C5 JUX B1201 " 0.042 2.00e-02 2.50e+03 pdb=" C9 JUX B1201 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N JUX A1201 " -0.109 2.00e-02 2.50e+03 9.67e-02 1.40e+02 pdb=" CA JUX A1201 " 0.135 2.00e-02 2.50e+03 pdb=" OH JUX A1201 " 0.130 2.00e-02 2.50e+03 pdb=" C1 JUX A1201 " -0.033 2.00e-02 2.50e+03 pdb=" C5 JUX A1201 " -0.051 2.00e-02 2.50e+03 pdb=" C9 JUX A1201 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 236 " -0.025 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO A 237 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.022 5.00e-02 4.00e+02 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 59 2.57 - 3.15: 7531 3.15 - 3.74: 12544 3.74 - 4.32: 14879 4.32 - 4.90: 25317 Nonbonded interactions: 60330 Sorted by model distance: nonbonded pdb=" OH TYR B 292 " pdb=" OG SER B 468 " model vdw 1.990 3.040 nonbonded pdb=" OH TYR A 292 " pdb=" OG SER A 468 " model vdw 1.995 3.040 nonbonded pdb=" OG SER A 345 " pdb=" OD1 ASN A 347 " model vdw 1.997 3.040 nonbonded pdb=" OG SER B 345 " pdb=" OD1 ASN B 347 " model vdw 1.999 3.040 nonbonded pdb=" O6 NAG F 1 " pdb=" O5 NAG F 2 " model vdw 2.093 3.040 ... (remaining 60325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.730 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 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 : 0.008 0.334 7866 Z= 0.415 Angle : 0.633 15.643 10840 Z= 0.282 Chirality : 0.038 0.186 1378 Planarity : 0.005 0.099 1328 Dihedral : 16.783 114.025 2624 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 50.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.28 % Allowed : 17.98 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.88 (0.28), residues: 1080 helix: 3.18 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.75 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 616 HIS 0.001 0.000 HIS A 344 PHE 0.007 0.001 PHE A 541 TYR 0.006 0.001 TYR A 186 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 1.41506 ( 12) link_BETA1-4 : bond 0.00601 ( 4) link_BETA1-4 : angle 1.76805 ( 12) hydrogen bonds : bond 0.12721 ( 515) hydrogen bonds : angle 4.87794 ( 1509) SS BOND : bond 0.00087 ( 6) SS BOND : angle 1.74966 ( 12) covalent geometry : bond 0.00833 ( 7852) covalent geometry : angle 0.62655 (10804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 0.725 Fit side-chains REVERT: A 410 LEU cc_start: 0.7355 (mt) cc_final: 0.6821 (tp) REVERT: A 571 ILE cc_start: 0.7071 (mm) cc_final: 0.6725 (mt) REVERT: A 583 MET cc_start: 0.7334 (mmm) cc_final: 0.6946 (mmm) REVERT: B 357 PHE cc_start: 0.5113 (m-80) cc_final: 0.4851 (t80) REVERT: B 410 LEU cc_start: 0.7478 (mt) cc_final: 0.7037 (tp) REVERT: B 411 TYR cc_start: 0.8196 (m-10) cc_final: 0.7992 (m-80) REVERT: B 528 ARG cc_start: 0.7469 (mpt-90) cc_final: 0.7259 (mmt90) REVERT: B 571 ILE cc_start: 0.7164 (mm) cc_final: 0.6844 (mt) REVERT: B 583 MET cc_start: 0.7313 (mmm) cc_final: 0.6864 (mmm) REVERT: B 643 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5802 (mt) outliers start: 2 outliers final: 0 residues processed: 200 average time/residue: 0.1438 time to fit residues: 41.8710 Evaluate side-chains 130 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 250 ASN B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.179543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152626 restraints weight = 9694.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156215 restraints weight = 5557.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158184 restraints weight = 3872.369| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7866 Z= 0.170 Angle : 0.768 8.707 10840 Z= 0.366 Chirality : 0.047 0.220 1378 Planarity : 0.005 0.064 1328 Dihedral : 13.746 98.920 1326 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.20 % Allowed : 21.35 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.03 (0.27), residues: 1080 helix: 2.22 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -1.74 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.001 0.000 HIS A 344 PHE 0.017 0.002 PHE A 541 TYR 0.010 0.001 TYR A 186 ARG 0.003 0.001 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 4) link_NAG-ASN : angle 2.05550 ( 12) link_BETA1-4 : bond 0.01605 ( 4) link_BETA1-4 : angle 4.39351 ( 12) hydrogen bonds : bond 0.04985 ( 515) hydrogen bonds : angle 4.11832 ( 1509) SS BOND : bond 0.00499 ( 6) SS BOND : angle 2.17915 ( 12) covalent geometry : bond 0.00390 ( 7852) covalent geometry : angle 0.74829 (10804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.696 Fit side-chains REVERT: A 571 ILE cc_start: 0.8538 (mm) cc_final: 0.8233 (mt) REVERT: A 573 SER cc_start: 0.7566 (t) cc_final: 0.7286 (t) REVERT: B 130 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7902 (tm-30) REVERT: B 197 PHE cc_start: 0.6565 (m-80) cc_final: 0.6363 (m-80) REVERT: B 571 ILE cc_start: 0.8471 (mm) cc_final: 0.8189 (mt) outliers start: 37 outliers final: 24 residues processed: 171 average time/residue: 0.1528 time to fit residues: 38.1268 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 619 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154085 restraints weight = 9898.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157542 restraints weight = 5756.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159446 restraints weight = 4069.863| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7866 Z= 0.162 Angle : 0.707 9.262 10840 Z= 0.339 Chirality : 0.046 0.225 1378 Planarity : 0.005 0.051 1328 Dihedral : 12.773 91.603 1324 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.88 % Allowed : 20.65 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.82 (0.26), residues: 1080 helix: 2.05 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.80 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 501 HIS 0.002 0.001 HIS B 394 PHE 0.014 0.002 PHE A 541 TYR 0.009 0.001 TYR A 186 ARG 0.003 0.001 ARG B 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 4) link_NAG-ASN : angle 1.67234 ( 12) link_BETA1-4 : bond 0.01491 ( 4) link_BETA1-4 : angle 4.61492 ( 12) hydrogen bonds : bond 0.04945 ( 515) hydrogen bonds : angle 4.02784 ( 1509) SS BOND : bond 0.00099 ( 6) SS BOND : angle 2.13032 ( 12) covalent geometry : bond 0.00385 ( 7852) covalent geometry : angle 0.68494 (10804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.826 Fit side-chains REVERT: A 137 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8207 (tp) REVERT: A 571 ILE cc_start: 0.8698 (mm) cc_final: 0.8425 (mt) REVERT: A 630 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8104 (ptm) REVERT: B 137 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8226 (tp) REVERT: B 223 ILE cc_start: 0.8533 (mm) cc_final: 0.8323 (mt) REVERT: B 571 ILE cc_start: 0.8674 (mm) cc_final: 0.8414 (mt) outliers start: 49 outliers final: 28 residues processed: 177 average time/residue: 0.1436 time to fit residues: 37.4992 Evaluate side-chains 161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 619 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 0.3980 chunk 11 optimal weight: 0.0170 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 100 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.184101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157464 restraints weight = 9722.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161048 restraints weight = 5643.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163326 restraints weight = 3962.709| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7866 Z= 0.135 Angle : 0.689 9.604 10840 Z= 0.324 Chirality : 0.044 0.246 1378 Planarity : 0.005 0.054 1328 Dihedral : 12.038 85.634 1324 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.62 % Allowed : 22.89 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.95 (0.27), residues: 1080 helix: 2.03 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.65 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.002 0.000 HIS B 394 PHE 0.019 0.001 PHE A 591 TYR 0.007 0.001 TYR A 186 ARG 0.003 0.001 ARG A 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 4) link_NAG-ASN : angle 1.67769 ( 12) link_BETA1-4 : bond 0.01659 ( 4) link_BETA1-4 : angle 4.81503 ( 12) hydrogen bonds : bond 0.04447 ( 515) hydrogen bonds : angle 3.83054 ( 1509) SS BOND : bond 0.00539 ( 6) SS BOND : angle 2.01647 ( 12) covalent geometry : bond 0.00289 ( 7852) covalent geometry : angle 0.66527 (10804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.781 Fit side-chains REVERT: A 137 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8131 (tp) REVERT: A 155 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7471 (tt) REVERT: A 571 ILE cc_start: 0.8656 (mm) cc_final: 0.8387 (mt) REVERT: A 630 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8136 (ptm) REVERT: B 137 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8146 (tp) REVERT: B 155 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7441 (tt) REVERT: B 197 PHE cc_start: 0.6545 (m-80) cc_final: 0.6310 (m-80) REVERT: B 571 ILE cc_start: 0.8630 (mm) cc_final: 0.8362 (mt) outliers start: 40 outliers final: 24 residues processed: 175 average time/residue: 0.1404 time to fit residues: 36.2669 Evaluate side-chains 162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.0270 chunk 89 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.183140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156671 restraints weight = 9739.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160155 restraints weight = 5656.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162385 restraints weight = 3990.987| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7866 Z= 0.135 Angle : 0.683 9.702 10840 Z= 0.319 Chirality : 0.044 0.256 1378 Planarity : 0.005 0.056 1328 Dihedral : 11.529 80.906 1324 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.76 % Allowed : 23.88 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.04 (0.27), residues: 1080 helix: 2.10 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.62 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.001 0.000 HIS B 394 PHE 0.018 0.001 PHE A 428 TYR 0.005 0.001 TYR A 186 ARG 0.002 0.001 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 4) link_NAG-ASN : angle 1.58628 ( 12) link_BETA1-4 : bond 0.01681 ( 4) link_BETA1-4 : angle 4.91706 ( 12) hydrogen bonds : bond 0.04374 ( 515) hydrogen bonds : angle 3.77458 ( 1509) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.90746 ( 12) covalent geometry : bond 0.00299 ( 7852) covalent geometry : angle 0.65921 (10804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.803 Fit side-chains REVERT: A 137 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8156 (tp) REVERT: A 571 ILE cc_start: 0.8664 (mm) cc_final: 0.8425 (mt) REVERT: A 630 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8113 (ptm) REVERT: B 137 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 571 ILE cc_start: 0.8635 (mm) cc_final: 0.8380 (mt) outliers start: 41 outliers final: 23 residues processed: 162 average time/residue: 0.1421 time to fit residues: 34.0143 Evaluate side-chains 151 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 9 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.182667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155986 restraints weight = 9906.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159500 restraints weight = 5712.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161752 restraints weight = 4019.503| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7866 Z= 0.142 Angle : 0.691 9.742 10840 Z= 0.322 Chirality : 0.044 0.258 1378 Planarity : 0.005 0.057 1328 Dihedral : 11.161 84.067 1324 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.18 % Allowed : 23.74 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.06 (0.27), residues: 1080 helix: 2.11 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.58 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 501 HIS 0.001 0.000 HIS B 344 PHE 0.023 0.001 PHE B 591 TYR 0.006 0.001 TYR A 186 ARG 0.002 0.000 ARG B 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 4) link_NAG-ASN : angle 1.71126 ( 12) link_BETA1-4 : bond 0.01702 ( 4) link_BETA1-4 : angle 5.01720 ( 12) hydrogen bonds : bond 0.04456 ( 515) hydrogen bonds : angle 3.78107 ( 1509) SS BOND : bond 0.00159 ( 6) SS BOND : angle 1.87264 ( 12) covalent geometry : bond 0.00327 ( 7852) covalent geometry : angle 0.66668 (10804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.807 Fit side-chains REVERT: A 137 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8146 (tp) REVERT: A 571 ILE cc_start: 0.8686 (mm) cc_final: 0.8468 (mt) REVERT: A 630 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8101 (ptm) REVERT: B 137 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8174 (tp) REVERT: B 571 ILE cc_start: 0.8652 (mm) cc_final: 0.8421 (mt) REVERT: B 643 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7368 (mt) outliers start: 44 outliers final: 37 residues processed: 163 average time/residue: 0.1457 time to fit residues: 34.9206 Evaluate side-chains 166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 31 optimal weight: 0.0070 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.181636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155412 restraints weight = 9775.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158946 restraints weight = 5633.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161140 restraints weight = 3958.994| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7866 Z= 0.136 Angle : 0.685 9.747 10840 Z= 0.318 Chirality : 0.044 0.262 1378 Planarity : 0.005 0.057 1328 Dihedral : 10.751 89.426 1324 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 6.60 % Allowed : 23.60 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.27), residues: 1080 helix: 2.09 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.52 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 339 HIS 0.001 0.000 HIS B 344 PHE 0.022 0.001 PHE A 591 TYR 0.006 0.001 TYR A 186 ARG 0.002 0.000 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 4) link_NAG-ASN : angle 1.66592 ( 12) link_BETA1-4 : bond 0.01712 ( 4) link_BETA1-4 : angle 5.12871 ( 12) hydrogen bonds : bond 0.04427 ( 515) hydrogen bonds : angle 3.73796 ( 1509) SS BOND : bond 0.00172 ( 6) SS BOND : angle 2.07183 ( 12) covalent geometry : bond 0.00309 ( 7852) covalent geometry : angle 0.65840 (10804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.745 Fit side-chains REVERT: A 137 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8143 (tp) REVERT: A 155 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 248 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 571 ILE cc_start: 0.8681 (mm) cc_final: 0.8449 (mt) REVERT: A 630 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8097 (ptm) REVERT: B 137 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8229 (tp) REVERT: B 248 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7893 (mp) REVERT: B 571 ILE cc_start: 0.8640 (mm) cc_final: 0.8422 (mt) REVERT: B 643 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7386 (mt) outliers start: 47 outliers final: 34 residues processed: 167 average time/residue: 0.1407 time to fit residues: 34.7518 Evaluate side-chains 162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 100 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 0.0670 chunk 102 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.183077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157503 restraints weight = 9899.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.160838 restraints weight = 5788.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162621 restraints weight = 4099.837| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7866 Z= 0.133 Angle : 0.697 9.728 10840 Z= 0.323 Chirality : 0.044 0.260 1378 Planarity : 0.005 0.057 1328 Dihedral : 10.347 89.274 1324 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.62 % Allowed : 24.72 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.14 (0.27), residues: 1080 helix: 2.13 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.49 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 501 HIS 0.000 0.000 HIS B 344 PHE 0.016 0.001 PHE A 591 TYR 0.005 0.001 TYR A 186 ARG 0.002 0.000 ARG A 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 4) link_NAG-ASN : angle 1.67582 ( 12) link_BETA1-4 : bond 0.01700 ( 4) link_BETA1-4 : angle 5.23579 ( 12) hydrogen bonds : bond 0.04280 ( 515) hydrogen bonds : angle 3.70211 ( 1509) SS BOND : bond 0.00220 ( 6) SS BOND : angle 2.09252 ( 12) covalent geometry : bond 0.00296 ( 7852) covalent geometry : angle 0.67013 (10804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.717 Fit side-chains REVERT: A 137 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8071 (tp) REVERT: A 248 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 630 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8195 (ptt) REVERT: B 137 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8188 (tp) REVERT: B 155 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7420 (tt) REVERT: B 571 ILE cc_start: 0.8611 (mm) cc_final: 0.8396 (mt) REVERT: B 643 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7360 (mt) outliers start: 40 outliers final: 26 residues processed: 157 average time/residue: 0.1407 time to fit residues: 32.6865 Evaluate side-chains 151 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 0.0050 chunk 105 optimal weight: 2.9990 chunk 96 optimal weight: 0.0370 chunk 74 optimal weight: 5.9990 chunk 38 optimal weight: 0.0570 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.159776 restraints weight = 9992.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163446 restraints weight = 5733.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.165755 restraints weight = 3977.135| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7866 Z= 0.129 Angle : 0.694 9.741 10840 Z= 0.320 Chirality : 0.043 0.253 1378 Planarity : 0.005 0.057 1328 Dihedral : 9.913 89.563 1324 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.34 % Allowed : 25.56 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.21 (0.27), residues: 1080 helix: 2.19 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.47 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 501 HIS 0.001 0.000 HIS B 344 PHE 0.016 0.001 PHE A 591 TYR 0.005 0.001 TYR A 186 ARG 0.002 0.000 ARG B 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 4) link_NAG-ASN : angle 1.67819 ( 12) link_BETA1-4 : bond 0.01725 ( 4) link_BETA1-4 : angle 5.35251 ( 12) hydrogen bonds : bond 0.04146 ( 515) hydrogen bonds : angle 3.66275 ( 1509) SS BOND : bond 0.00168 ( 6) SS BOND : angle 2.05211 ( 12) covalent geometry : bond 0.00285 ( 7852) covalent geometry : angle 0.66598 (10804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.795 Fit side-chains REVERT: A 137 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 137 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 155 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7347 (tt) REVERT: B 248 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 571 ILE cc_start: 0.8566 (mm) cc_final: 0.8336 (mt) REVERT: B 643 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7342 (mt) outliers start: 38 outliers final: 25 residues processed: 155 average time/residue: 0.1482 time to fit residues: 33.9676 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 chunk 88 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.182853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156558 restraints weight = 9956.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160172 restraints weight = 5713.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162394 restraints weight = 3985.398| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7866 Z= 0.140 Angle : 0.722 9.869 10840 Z= 0.330 Chirality : 0.044 0.237 1378 Planarity : 0.005 0.056 1328 Dihedral : 9.516 88.392 1324 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.63 % Allowed : 26.69 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.18 (0.27), residues: 1080 helix: 2.16 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.48 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 501 HIS 0.001 0.000 HIS B 394 PHE 0.017 0.001 PHE A 591 TYR 0.006 0.001 TYR A 186 ARG 0.002 0.000 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 4) link_NAG-ASN : angle 1.68678 ( 12) link_BETA1-4 : bond 0.01720 ( 4) link_BETA1-4 : angle 5.43536 ( 12) hydrogen bonds : bond 0.04341 ( 515) hydrogen bonds : angle 3.69420 ( 1509) SS BOND : bond 0.00165 ( 6) SS BOND : angle 2.09076 ( 12) covalent geometry : bond 0.00327 ( 7852) covalent geometry : angle 0.69475 (10804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.711 Fit side-chains REVERT: A 137 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 248 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7826 (mp) REVERT: B 137 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8230 (tp) REVERT: B 155 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7420 (tt) REVERT: B 248 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7932 (mp) REVERT: B 571 ILE cc_start: 0.8611 (mm) cc_final: 0.8399 (mt) outliers start: 33 outliers final: 27 residues processed: 149 average time/residue: 0.1511 time to fit residues: 33.6908 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 28 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.184102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158151 restraints weight = 9821.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161696 restraints weight = 5600.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.163945 restraints weight = 3911.604| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7866 Z= 0.133 Angle : 0.718 9.738 10840 Z= 0.327 Chirality : 0.043 0.226 1378 Planarity : 0.005 0.056 1328 Dihedral : 9.173 88.120 1324 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.78 % Allowed : 26.54 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.24 (0.27), residues: 1080 helix: 2.22 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.47 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 501 HIS 0.000 0.000 HIS B 344 PHE 0.019 0.001 PHE B 428 TYR 0.005 0.001 TYR A 186 ARG 0.002 0.000 ARG B 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 4) link_NAG-ASN : angle 1.66680 ( 12) link_BETA1-4 : bond 0.01744 ( 4) link_BETA1-4 : angle 5.56643 ( 12) hydrogen bonds : bond 0.04251 ( 515) hydrogen bonds : angle 3.66186 ( 1509) SS BOND : bond 0.00136 ( 6) SS BOND : angle 2.05949 ( 12) covalent geometry : bond 0.00302 ( 7852) covalent geometry : angle 0.68930 (10804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2485.16 seconds wall clock time: 43 minutes 59.89 seconds (2639.89 seconds total)