Starting phenix.real_space_refine on Tue Mar 3 18:10:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tti_26116/03_2026/7tti_26116_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tti_26116/03_2026/7tti_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_26116/03_2026/7tti_26116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tti_26116/03_2026/7tti_26116.map" model { file = "/net/cci-nas-00/data/ceres_data/7tti_26116/03_2026/7tti_26116_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tti_26116/03_2026/7tti_26116_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 8, 'GLU:plan': 8, 'PHE:plan': 7, 'TYR:plan': 5, 'HIS:plan': 2, 'ASP:plan': 11, 'ASN:plan1': 4, 'GLN:plan1': 5, 'TRP:plan': 1} 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: {'ARG:plan': 8, 'GLU:plan': 8, 'PHE:plan': 7, 'TYR:plan': 5, 'HIS:plan': 2, 'ASP:plan': 11, 'ASN:plan1': 4, 'GLN:plan1': 5, 'TRP:plan': 1} 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: 1.83, per 1000 atoms: 0.24 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: 0.81 Conformation dependent library (CDL) restraints added in 334.2 milliseconds 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: 0.24 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: 1.40 Time building geometry restraints manager: 0.95 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: 0.01 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.170 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- 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 : 50.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG A 140 TYR 0.006 0.001 TYR A 186 PHE 0.007 0.001 PHE A 541 TRP 0.004 0.001 TRP B 616 HIS 0.001 0.000 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00833 ( 7852) covalent geometry : angle 0.62655 (10804) SS BOND : bond 0.00087 ( 6) SS BOND : angle 1.74966 ( 12) hydrogen bonds : bond 0.12721 ( 515) hydrogen bonds : angle 4.87794 ( 1509) link_BETA1-4 : bond 0.00601 ( 4) link_BETA1-4 : angle 1.76805 ( 12) link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 1.41506 ( 12) *********************** 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 : 0.196 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: 0.0591 time to fit residues: 17.6013 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 : 0.262 ------------------------------------------------------------------------------- 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 49 optimal weight: 40.0000 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.182146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156046 restraints weight = 9599.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159375 restraints weight = 5709.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161553 restraints weight = 4071.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.162652 restraints weight = 3239.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163656 restraints weight = 2835.937| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7866 Z= 0.156 Angle : 0.749 8.675 10840 Z= 0.356 Chirality : 0.046 0.215 1378 Planarity : 0.005 0.064 1328 Dihedral : 13.746 98.983 1326 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.34 % Allowed : 21.35 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.27), residues: 1080 helix: 2.28 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.70 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 528 TYR 0.009 0.001 TYR A 637 PHE 0.016 0.002 PHE B 428 TRP 0.011 0.001 TRP B 339 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7852) covalent geometry : angle 0.72935 (10804) SS BOND : bond 0.00706 ( 6) SS BOND : angle 2.13026 ( 12) hydrogen bonds : bond 0.04863 ( 515) hydrogen bonds : angle 4.09032 ( 1509) link_BETA1-4 : bond 0.01509 ( 4) link_BETA1-4 : angle 4.39618 ( 12) link_NAG-ASN : bond 0.00115 ( 4) link_NAG-ASN : angle 2.06009 ( 12) *********************** 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 185 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.250 Fit side-chains REVERT: A 571 ILE cc_start: 0.8488 (mm) cc_final: 0.8204 (mt) REVERT: B 130 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 571 ILE cc_start: 0.8452 (mm) cc_final: 0.8167 (mt) outliers start: 38 outliers final: 21 residues processed: 172 average time/residue: 0.0620 time to fit residues: 15.7057 Evaluate side-chains 154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 339 TRP 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.180784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155457 restraints weight = 9541.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158937 restraints weight = 5436.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161166 restraints weight = 3767.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162260 restraints weight = 2970.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163217 restraints weight = 2587.479| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7866 Z= 0.148 Angle : 0.705 9.445 10840 Z= 0.333 Chirality : 0.045 0.215 1378 Planarity : 0.005 0.050 1328 Dihedral : 12.904 93.076 1324 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.34 % Allowed : 22.05 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1080 helix: 2.20 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -1.80 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 440 TYR 0.007 0.001 TYR B 411 PHE 0.014 0.001 PHE A 541 TRP 0.007 0.001 TRP B 501 HIS 0.001 0.000 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7852) covalent geometry : angle 0.68342 (10804) SS BOND : bond 0.00059 ( 6) SS BOND : angle 2.06739 ( 12) hydrogen bonds : bond 0.04683 ( 515) hydrogen bonds : angle 3.97864 ( 1509) link_BETA1-4 : bond 0.01575 ( 4) link_BETA1-4 : angle 4.63185 ( 12) link_NAG-ASN : bond 0.00149 ( 4) link_NAG-ASN : angle 1.75770 ( 12) *********************** 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 179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.171 Fit side-chains REVERT: A 137 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8099 (tp) REVERT: A 223 ILE cc_start: 0.8455 (mm) cc_final: 0.8173 (mm) REVERT: A 571 ILE cc_start: 0.8643 (mm) cc_final: 0.8348 (mt) REVERT: B 137 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8142 (tp) REVERT: B 223 ILE cc_start: 0.8502 (mm) cc_final: 0.8267 (mt) REVERT: B 571 ILE cc_start: 0.8589 (mm) cc_final: 0.8330 (mt) outliers start: 38 outliers final: 21 residues processed: 168 average time/residue: 0.0580 time to fit residues: 14.6115 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 287 SER 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 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 287 SER Chi-restraints excluded: chain B residue 424 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 103 optimal weight: 40.0000 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.184434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157213 restraints weight = 9995.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.160800 restraints weight = 5746.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.162841 restraints weight = 4027.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164473 restraints weight = 3231.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165027 restraints weight = 2767.284| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7866 Z= 0.139 Angle : 0.685 9.667 10840 Z= 0.324 Chirality : 0.044 0.246 1378 Planarity : 0.005 0.053 1328 Dihedral : 12.054 85.716 1324 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.32 % Allowed : 21.49 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1080 helix: 2.12 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -1.68 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 528 TYR 0.006 0.001 TYR A 186 PHE 0.021 0.002 PHE A 591 TRP 0.007 0.001 TRP B 339 HIS 0.002 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7852) covalent geometry : angle 0.66221 (10804) SS BOND : bond 0.00367 ( 6) SS BOND : angle 1.92833 ( 12) hydrogen bonds : bond 0.04513 ( 515) hydrogen bonds : angle 3.82904 ( 1509) link_BETA1-4 : bond 0.01590 ( 4) link_BETA1-4 : angle 4.79604 ( 12) link_NAG-ASN : bond 0.00156 ( 4) link_NAG-ASN : angle 1.68757 ( 12) *********************** 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 185 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.244 Fit side-chains REVERT: A 137 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8138 (tp) REVERT: A 155 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7468 (tt) REVERT: A 571 ILE cc_start: 0.8670 (mm) cc_final: 0.8407 (mt) REVERT: B 137 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 155 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7458 (tt) REVERT: B 571 ILE cc_start: 0.8687 (mm) cc_final: 0.8446 (mt) outliers start: 45 outliers final: 25 residues processed: 174 average time/residue: 0.0596 time to fit residues: 15.4888 Evaluate side-chains 159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain A residue 362 VAL 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 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 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 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 507 ILE Chi-restraints excluded: chain B residue 619 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 0.0020 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.182637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155899 restraints weight = 9810.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159357 restraints weight = 5717.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.161620 restraints weight = 4062.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162913 restraints weight = 3218.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163925 restraints weight = 2775.322| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7866 Z= 0.138 Angle : 0.696 9.698 10840 Z= 0.323 Chirality : 0.044 0.253 1378 Planarity : 0.005 0.055 1328 Dihedral : 11.543 82.025 1324 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.18 % Allowed : 24.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.27), residues: 1080 helix: 1.98 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -1.54 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 252 TYR 0.006 0.001 TYR A 186 PHE 0.016 0.001 PHE A 591 TRP 0.007 0.001 TRP B 501 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7852) covalent geometry : angle 0.67267 (10804) SS BOND : bond 0.00175 ( 6) SS BOND : angle 1.87323 ( 12) hydrogen bonds : bond 0.04433 ( 515) hydrogen bonds : angle 3.80593 ( 1509) link_BETA1-4 : bond 0.01654 ( 4) link_BETA1-4 : angle 4.91754 ( 12) link_NAG-ASN : bond 0.00118 ( 4) link_NAG-ASN : angle 1.66356 ( 12) *********************** 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 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.171 Fit side-chains REVERT: A 137 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8152 (tp) REVERT: A 571 ILE cc_start: 0.8674 (mm) cc_final: 0.8427 (mt) REVERT: B 137 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8152 (tp) REVERT: B 571 ILE cc_start: 0.8662 (mm) cc_final: 0.8422 (mt) outliers start: 44 outliers final: 31 residues processed: 166 average time/residue: 0.0561 time to fit residues: 13.9359 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 287 SER Chi-restraints excluded: chain A residue 362 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 570 LEU Chi-restraints excluded: chain A residue 619 SER 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 287 SER 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 619 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.181104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154317 restraints weight = 9946.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157859 restraints weight = 5777.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160073 restraints weight = 4070.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161200 restraints weight = 3245.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.162159 restraints weight = 2840.110| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7866 Z= 0.151 Angle : 0.696 9.735 10840 Z= 0.327 Chirality : 0.045 0.261 1378 Planarity : 0.005 0.056 1328 Dihedral : 11.183 89.414 1324 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 6.04 % Allowed : 24.02 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1080 helix: 2.07 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 252 TYR 0.007 0.001 TYR A 186 PHE 0.023 0.002 PHE B 591 TRP 0.005 0.001 TRP B 339 HIS 0.001 0.000 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7852) covalent geometry : angle 0.67160 (10804) SS BOND : bond 0.00195 ( 6) SS BOND : angle 1.89972 ( 12) hydrogen bonds : bond 0.04661 ( 515) hydrogen bonds : angle 3.80032 ( 1509) link_BETA1-4 : bond 0.01716 ( 4) link_BETA1-4 : angle 5.02090 ( 12) link_NAG-ASN : bond 0.00124 ( 4) link_NAG-ASN : angle 1.61980 ( 12) *********************** 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 169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.278 Fit side-chains REVERT: A 137 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8199 (tp) REVERT: A 571 ILE cc_start: 0.8679 (mm) cc_final: 0.8472 (mt) REVERT: B 137 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8163 (tp) REVERT: B 571 ILE cc_start: 0.8684 (mm) cc_final: 0.8468 (mt) outliers start: 43 outliers final: 34 residues processed: 159 average time/residue: 0.0571 time to fit residues: 13.7123 Evaluate side-chains 158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 362 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 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 221 ILE Chi-restraints excluded: chain B residue 287 SER 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 654 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.182038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155540 restraints weight = 9859.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159044 restraints weight = 5691.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161271 restraints weight = 4001.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162372 restraints weight = 3185.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.163498 restraints weight = 2787.108| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7866 Z= 0.142 Angle : 0.694 9.734 10840 Z= 0.324 Chirality : 0.044 0.261 1378 Planarity : 0.005 0.056 1328 Dihedral : 10.746 86.896 1324 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 6.04 % Allowed : 25.00 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.27), residues: 1080 helix: 2.09 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 252 TYR 0.007 0.001 TYR A 186 PHE 0.018 0.001 PHE A 591 TRP 0.006 0.001 TRP B 501 HIS 0.001 0.000 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7852) covalent geometry : angle 0.66827 (10804) SS BOND : bond 0.00144 ( 6) SS BOND : angle 1.91897 ( 12) hydrogen bonds : bond 0.04583 ( 515) hydrogen bonds : angle 3.76636 ( 1509) link_BETA1-4 : bond 0.01686 ( 4) link_BETA1-4 : angle 5.11605 ( 12) link_NAG-ASN : bond 0.00166 ( 4) link_NAG-ASN : angle 1.61259 ( 12) *********************** 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 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.260 Fit side-chains REVERT: A 137 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8221 (tp) REVERT: A 155 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7459 (tt) REVERT: A 248 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7856 (mp) REVERT: A 571 ILE cc_start: 0.8663 (mm) cc_final: 0.8447 (mt) REVERT: A 630 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8173 (ptm) REVERT: B 137 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 248 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 571 ILE cc_start: 0.8669 (mm) cc_final: 0.8454 (mt) outliers start: 43 outliers final: 34 residues processed: 163 average time/residue: 0.0589 time to fit residues: 14.3599 Evaluate side-chains 163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 362 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 221 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 287 SER 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 654 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.6980 chunk 103 optimal weight: 30.0000 chunk 85 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.0060 chunk 43 optimal weight: 0.5980 chunk 6 optimal weight: 0.0370 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.3874 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.184221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157646 restraints weight = 9927.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161242 restraints weight = 5729.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163322 restraints weight = 4018.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.164910 restraints weight = 3218.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165181 restraints weight = 2751.307| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7866 Z= 0.132 Angle : 0.698 9.761 10840 Z= 0.320 Chirality : 0.044 0.261 1378 Planarity : 0.005 0.057 1328 Dihedral : 10.205 86.280 1324 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.62 % Allowed : 25.14 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.27), residues: 1080 helix: 2.12 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.50 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 252 TYR 0.007 0.001 TYR B 411 PHE 0.019 0.001 PHE A 591 TRP 0.009 0.001 TRP B 501 HIS 0.001 0.000 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7852) covalent geometry : angle 0.67119 (10804) SS BOND : bond 0.00143 ( 6) SS BOND : angle 2.04225 ( 12) hydrogen bonds : bond 0.04329 ( 515) hydrogen bonds : angle 3.71601 ( 1509) link_BETA1-4 : bond 0.01684 ( 4) link_BETA1-4 : angle 5.22002 ( 12) link_NAG-ASN : bond 0.00202 ( 4) link_NAG-ASN : angle 1.70969 ( 12) *********************** 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 168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.265 Fit side-chains REVERT: A 137 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8096 (tp) REVERT: A 571 ILE cc_start: 0.8606 (mm) cc_final: 0.8399 (mt) REVERT: A 630 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8175 (ptm) REVERT: B 137 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8149 (tp) REVERT: B 571 ILE cc_start: 0.8647 (mm) cc_final: 0.8431 (mt) outliers start: 40 outliers final: 31 residues processed: 161 average time/residue: 0.0608 time to fit residues: 14.7229 Evaluate side-chains 156 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 339 TRP Chi-restraints excluded: chain A residue 362 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 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 654 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.175117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148895 restraints weight = 9944.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152103 restraints weight = 5766.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154305 restraints weight = 4115.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155380 restraints weight = 3290.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156297 restraints weight = 2886.926| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7866 Z= 0.189 Angle : 0.755 10.049 10840 Z= 0.357 Chirality : 0.047 0.250 1378 Planarity : 0.005 0.057 1328 Dihedral : 9.796 89.444 1324 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 6.04 % Allowed : 25.00 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1080 helix: 1.88 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 252 TYR 0.010 0.001 TYR A 186 PHE 0.028 0.002 PHE A 591 TRP 0.006 0.001 TRP B 501 HIS 0.001 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 7852) covalent geometry : angle 0.73004 (10804) SS BOND : bond 0.00278 ( 6) SS BOND : angle 2.19501 ( 12) hydrogen bonds : bond 0.05208 ( 515) hydrogen bonds : angle 3.91714 ( 1509) link_BETA1-4 : bond 0.01678 ( 4) link_BETA1-4 : angle 5.32820 ( 12) link_NAG-ASN : bond 0.00117 ( 4) link_NAG-ASN : angle 1.45564 ( 12) *********************** 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 163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 0.296 Fit side-chains REVERT: A 137 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 248 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7907 (mp) REVERT: A 573 SER cc_start: 0.7503 (t) cc_final: 0.7206 (t) REVERT: A 630 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8109 (ptm) REVERT: B 137 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8425 (tp) REVERT: B 248 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8000 (mp) REVERT: B 573 SER cc_start: 0.7503 (t) cc_final: 0.7219 (t) REVERT: B 643 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7409 (mt) outliers start: 43 outliers final: 33 residues processed: 157 average time/residue: 0.0606 time to fit residues: 14.0989 Evaluate side-chains 153 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 137 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 362 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 131 ASN 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 221 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 418 THR 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 643 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.177216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151018 restraints weight = 9893.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154404 restraints weight = 5745.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156209 restraints weight = 4053.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157720 restraints weight = 3297.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158232 restraints weight = 2838.346| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.004 0.048 7866 Z= 0.159 Angle : 0.750 9.767 10840 Z= 0.349 Chirality : 0.045 0.242 1378 Planarity : 0.005 0.059 1328 Dihedral : 9.548 89.218 1324 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.48 % Allowed : 26.12 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.27), residues: 1080 helix: 1.90 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.56 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 252 TYR 0.009 0.001 TYR A 186 PHE 0.024 0.002 PHE A 591 TRP 0.007 0.001 TRP B 501 HIS 0.001 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7852) covalent geometry : angle 0.72443 (10804) SS BOND : bond 0.00336 ( 6) SS BOND : angle 2.12023 ( 12) hydrogen bonds : bond 0.04998 ( 515) hydrogen bonds : angle 3.87178 ( 1509) link_BETA1-4 : bond 0.01660 ( 4) link_BETA1-4 : angle 5.42260 ( 12) link_NAG-ASN : bond 0.00153 ( 4) link_NAG-ASN : angle 1.49881 ( 12) ********************** 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 158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.194 Fit side-chains REVERT: A 137 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8283 (tp) REVERT: A 248 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7941 (mp) REVERT: A 573 SER cc_start: 0.7376 (t) cc_final: 0.7164 (t) REVERT: A 630 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8113 (ptm) REVERT: B 137 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8428 (tp) REVERT: B 248 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7984 (mp) REVERT: B 573 SER cc_start: 0.7329 (t) cc_final: 0.7105 (t) REVERT: B 643 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7365 (mt) outliers start: 39 outliers final: 32 residues processed: 152 average time/residue: 0.0541 time to fit residues: 12.4415 Evaluate side-chains 152 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 137 LEU Chi-restraints excluded: chain A residue 163 CYS 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151946 restraints weight = 9969.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155374 restraints weight = 5764.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157598 restraints weight = 4050.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158423 restraints weight = 3206.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159357 restraints weight = 2859.326| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7866 Z= 0.155 Angle : 0.743 9.806 10840 Z= 0.344 Chirality : 0.045 0.229 1378 Planarity : 0.005 0.059 1328 Dihedral : 8.946 89.943 1324 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.62 % Allowed : 25.98 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.27), residues: 1080 helix: 1.93 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.51 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 252 TYR 0.008 0.001 TYR A 186 PHE 0.021 0.002 PHE A 591 TRP 0.008 0.001 TRP B 501 HIS 0.000 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7852) covalent geometry : angle 0.71443 (10804) SS BOND : bond 0.00245 ( 6) SS BOND : angle 2.17867 ( 12) hydrogen bonds : bond 0.04809 ( 515) hydrogen bonds : angle 3.84502 ( 1509) link_BETA1-4 : bond 0.01724 ( 4) link_BETA1-4 : angle 5.60779 ( 12) link_NAG-ASN : bond 0.00196 ( 4) link_NAG-ASN : angle 1.60096 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1213.84 seconds wall clock time: 21 minutes 37.25 seconds (1297.25 seconds total)