Starting phenix.real_space_refine on Thu Jul 2 01:08:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uo9_42431/07_2026/8uo9_42431_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uo9_42431/07_2026/8uo9_42431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uo9_42431/07_2026/8uo9_42431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uo9_42431/07_2026/8uo9_42431.map" model { file = "/net/cci-nas-00/data/ceres_data/8uo9_42431/07_2026/8uo9_42431_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uo9_42431/07_2026/8uo9_42431_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 3286 2.51 5 N 833 2.21 5 O 919 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4304 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 14, 'TRANS': 540} Chain breaks: 3 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 587 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 4, 'ARG:plan': 8, 'PHE:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'TYR:plan': 5, 'ASP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 188 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'PS1': 1, 'X49': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 1.29, per 1000 atoms: 0.25 Number of scatterers: 5076 At special positions: 0 Unit cell: (95.256, 122.472, 97.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 1 15.00 F 6 9.00 O 919 8.00 N 833 7.00 C 3286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG D 1 " - " ASN A 573 " " NAG G 1 " - " ASN A 548 " " NAG I 1 " - " ASN A 498 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 135.5 milliseconds 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1226 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 57.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 146 through 160 removed outlier: 3.945A pdb=" N GLN A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 188 removed outlier: 3.921A pdb=" N TRP A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.519A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 250 removed outlier: 3.695A pdb=" N CYS A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 282 removed outlier: 3.920A pdb=" N GLY A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Proline residue: A 274 - end of helix removed outlier: 3.720A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 removed outlier: 3.987A pdb=" N ARG A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.890A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.603A pdb=" N PHE A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 337 " --> pdb=" O TRP A 333 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Proline residue: A 343 - end of helix removed outlier: 3.793A pdb=" N THR A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 removed outlier: 3.660A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 386 removed outlier: 3.509A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 385 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 438 Processing helix chain 'A' and resid 443 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 623 through 645 removed outlier: 3.857A pdb=" N PHE A 640 " --> pdb=" O CYS A 636 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 643 " --> pdb=" O CYS A 639 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 677 removed outlier: 3.697A pdb=" N ILE A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 removed outlier: 3.637A pdb=" N PHE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 731 removed outlier: 3.939A pdb=" N ALA A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 515 through 516 Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 532 removed outlier: 5.786A pdb=" N PHE A 526 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS A 549 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP A 528 " --> pdb=" O CYS A 549 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N PHE A 551 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N LEU A 530 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ASN A 553 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU A 532 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL A 555 " --> pdb=" O GLU A 532 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LEU A 571 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N THR A 550 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N ASN A 573 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE A 552 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N THR A 575 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A 554 " --> pdb=" O THR A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.681A pdb=" N THR A 559 " --> pdb=" O HIS A 578 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.155A pdb=" N VAL B 98 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL B 33 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N MET B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 308 hydrogen bonds defined for protein. 885 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: 0.57 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 797 1.31 - 1.44: 1533 1.44 - 1.57: 2815 1.57 - 1.70: 2 1.70 - 1.82: 50 Bond restraints: 5197 Sorted by residual: bond pdb=" C24 X49 A 801 " pdb=" N06 X49 A 801 " ideal model delta sigma weight residual 1.439 1.359 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C7 PS1 A 803 " pdb=" O7 PS1 A 803 " ideal model delta sigma weight residual 1.329 1.400 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C07 X49 A 801 " pdb=" C22 X49 A 801 " ideal model delta sigma weight residual 1.411 1.341 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N VAL B 63 " pdb=" CA VAL B 63 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.16e+01 bond pdb=" C17 PS1 A 803 " pdb=" O9 PS1 A 803 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 5192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 6946 3.51 - 7.01: 110 7.01 - 10.52: 12 10.52 - 14.02: 1 14.02 - 17.53: 1 Bond angle restraints: 7070 Sorted by residual: angle pdb=" N ARG B 32 " pdb=" CA ARG B 32 " pdb=" C ARG B 32 " ideal model delta sigma weight residual 108.67 98.68 9.99 1.55e+00 4.16e-01 4.16e+01 angle pdb=" C LYS B 86 " pdb=" N PRO B 87 " pdb=" CA PRO B 87 " ideal model delta sigma weight residual 119.47 126.72 -7.25 1.16e+00 7.43e-01 3.90e+01 angle pdb=" N THR B 101 " pdb=" CA THR B 101 " pdb=" C THR B 101 " ideal model delta sigma weight residual 110.19 117.85 -7.66 1.24e+00 6.50e-01 3.82e+01 angle pdb=" O3 PS1 A 803 " pdb=" P1 PS1 A 803 " pdb=" O6 PS1 A 803 " ideal model delta sigma weight residual 93.15 110.68 -17.53 3.00e+00 1.11e-01 3.41e+01 angle pdb=" N ALA B 52 " pdb=" CA ALA B 52 " pdb=" C ALA B 52 " ideal model delta sigma weight residual 111.71 118.09 -6.38 1.15e+00 7.56e-01 3.08e+01 ... (remaining 7065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 2984 35.08 - 70.15: 95 70.15 - 105.23: 26 105.23 - 140.31: 2 140.31 - 175.39: 1 Dihedral angle restraints: 3108 sinusoidal: 1194 harmonic: 1914 Sorted by residual: dihedral pdb=" CA LEU A 521 " pdb=" C LEU A 521 " pdb=" N LYS A 522 " pdb=" CA LYS A 522 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" C11 X49 A 801 " pdb=" C12 X49 A 801 " pdb=" C13 X49 A 801 " pdb=" C14 X49 A 801 " ideal model delta sinusoidal sigma weight residual 185.40 10.01 175.39 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C12 X49 A 801 " pdb=" C10 X49 A 801 " pdb=" C11 X49 A 801 " pdb=" N09 X49 A 801 " ideal model delta sinusoidal sigma weight residual 135.31 -88.93 -135.76 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 3105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.135: 813 1.135 - 2.270: 0 2.270 - 3.405: 0 3.405 - 4.540: 0 4.540 - 5.674: 1 Chirality restraints: 814 Sorted by residual: chirality pdb=" C11 X49 A 801 " pdb=" C10 X49 A 801 " pdb=" C12 X49 A 801 " pdb=" C19 X49 A 801 " both_signs ideal model delta sigma weight residual False -2.75 2.93 -5.67 2.00e-01 2.50e+01 8.05e+02 chirality pdb=" C5 NAG I 2 " pdb=" C4 NAG I 2 " pdb=" C6 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.41 -1.95 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.88e+00 ... (remaining 811 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG I 1 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.044 2.00e-02 2.50e+03 3.63e-02 1.65e+01 pdb=" C7 NAG I 2 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 161 " -0.021 2.00e-02 2.50e+03 1.80e-02 4.86e+00 pdb=" CG HIS A 161 " 0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS A 161 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS A 161 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 161 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 161 " -0.017 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1487 2.81 - 3.34: 5083 3.34 - 3.86: 8365 3.86 - 4.38: 9184 4.38 - 4.90: 15782 Nonbonded interactions: 39901 Sorted by model distance: nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.292 3.040 nonbonded pdb=" NZ LYS A 288 " pdb=" OD2 ASP A 620 " model vdw 2.322 3.120 nonbonded pdb=" OH TYR A 535 " pdb=" OE1 GLU A 537 " model vdw 2.349 3.040 nonbonded pdb=" OD1 ASP A 620 " pdb=" N LYS A 621 " model vdw 2.371 3.120 nonbonded pdb=" O GLN A 504 " pdb=" N SER A 525 " model vdw 2.400 3.120 ... (remaining 39896 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: 0.00 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 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: 0.210 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.310 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 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 : 0.006 0.080 5204 Z= 0.394 Angle : 1.021 17.527 7091 Z= 0.602 Chirality : 0.206 5.674 814 Planarity : 0.005 0.042 880 Dihedral : 19.504 175.385 1882 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 18.43 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.33), residues: 664 helix: 1.50 (0.27), residues: 351 sheet: -0.20 (0.64), residues: 65 loop : -1.59 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 626 TYR 0.011 0.001 TYR A 306 PHE 0.013 0.001 PHE A 245 TRP 0.010 0.001 TRP A 333 HIS 0.013 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.39 ( 5197) covalent geometry : angle 1.01309 / 0.60 ( 7070) hydrogen bonds : bond 0.12443 / 8.89 ( 301) hydrogen bonds : angle 5.74552 / 4.14 ( 885) link_BETA1-4 : bond 0.00373 / 0.18 ( 4) link_BETA1-4 : angle 2.44088 / 1.56 ( 12) link_NAG-ASN : bond 0.00579 / 0.29 ( 3) link_NAG-ASN : angle 2.68327 / 1.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 382 MET cc_start: 0.6339 (mmp) cc_final: 0.6106 (mmp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0523 time to fit residues: 5.3313 Evaluate side-chains 71 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS A 503 ASN A 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.211490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165736 restraints weight = 6725.969| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.99 r_work: 0.3883 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5204 Z= 0.197 Angle : 0.639 6.074 7091 Z= 0.322 Chirality : 0.044 0.220 814 Planarity : 0.004 0.042 880 Dihedral : 15.569 86.115 978 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.02 % Allowed : 18.20 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.33), residues: 664 helix: 1.50 (0.28), residues: 349 sheet: -0.19 (0.62), residues: 66 loop : -1.60 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.015 0.002 TYR A 461 PHE 0.018 0.002 PHE A 707 TRP 0.015 0.002 TRP A 333 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 5197) covalent geometry : angle 0.62566 / 0.32 ( 7070) hydrogen bonds : bond 0.05404 / 3.51 ( 301) hydrogen bonds : angle 4.71139 / 3.37 ( 885) link_BETA1-4 : bond 0.00702 / 0.35 ( 4) link_BETA1-4 : angle 2.92634 / 2.15 ( 12) link_NAG-ASN : bond 0.00698 / 0.34 ( 3) link_NAG-ASN : angle 1.69794 / 0.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 249 SER cc_start: 0.7531 (p) cc_final: 0.7262 (p) REVERT: A 315 ILE cc_start: 0.8010 (pt) cc_final: 0.7641 (mt) REVERT: A 334 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7150 (mmt180) REVERT: A 449 MET cc_start: 0.7235 (mmm) cc_final: 0.6870 (mmm) REVERT: A 626 ARG cc_start: 0.6711 (ptm160) cc_final: 0.6202 (ptm160) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.0612 time to fit residues: 6.0991 Evaluate side-chains 74 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 50.0000 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.213502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.167448 restraints weight = 6606.984| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.07 r_work: 0.3886 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5204 Z= 0.144 Angle : 0.550 7.343 7091 Z= 0.279 Chirality : 0.042 0.253 814 Planarity : 0.004 0.042 880 Dihedral : 13.868 75.788 978 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.12 % Allowed : 19.10 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.33), residues: 664 helix: 1.68 (0.28), residues: 348 sheet: 0.10 (0.62), residues: 66 loop : -1.35 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.014 0.001 TYR A 306 PHE 0.015 0.001 PHE A 245 TRP 0.012 0.001 TRP A 333 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 5197) covalent geometry : angle 0.53460 / 0.28 ( 7070) hydrogen bonds : bond 0.04648 / 3.01 ( 301) hydrogen bonds : angle 4.35722 / 3.12 ( 885) link_BETA1-4 : bond 0.00520 / 0.26 ( 4) link_BETA1-4 : angle 2.99668 / 2.14 ( 12) link_NAG-ASN : bond 0.00493 / 0.24 ( 3) link_NAG-ASN : angle 1.43907 / 0.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.7623 (tp) cc_final: 0.7395 (tp) REVERT: A 310 MET cc_start: 0.6500 (mmm) cc_final: 0.5524 (mmm) REVERT: A 315 ILE cc_start: 0.8066 (pt) cc_final: 0.7583 (mt) REVERT: A 334 ARG cc_start: 0.7574 (mtp85) cc_final: 0.7028 (mmt180) REVERT: A 392 PHE cc_start: 0.7776 (t80) cc_final: 0.7527 (t80) REVERT: A 449 MET cc_start: 0.7103 (mmm) cc_final: 0.6778 (mmm) REVERT: A 599 PHE cc_start: 0.7055 (t80) cc_final: 0.6833 (t80) outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 0.0511 time to fit residues: 5.0694 Evaluate side-chains 69 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 348 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 40.0000 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.211144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.164448 restraints weight = 6595.652| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.04 r_work: 0.3852 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5204 Z= 0.190 Angle : 0.593 8.233 7091 Z= 0.296 Chirality : 0.043 0.259 814 Planarity : 0.004 0.040 880 Dihedral : 12.449 81.320 978 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.70 % Allowed : 18.43 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.33), residues: 664 helix: 1.43 (0.27), residues: 354 sheet: 0.40 (0.63), residues: 66 loop : -1.22 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.015 0.002 TYR A 306 PHE 0.018 0.001 PHE A 459 TRP 0.014 0.002 TRP A 333 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 5197) covalent geometry : angle 0.57934 / 0.29 ( 7070) hydrogen bonds : bond 0.05133 / 3.30 ( 301) hydrogen bonds : angle 4.35321 / 3.14 ( 885) link_BETA1-4 : bond 0.00406 / 0.20 ( 4) link_BETA1-4 : angle 2.96868 / 2.09 ( 12) link_NAG-ASN : bond 0.00470 / 0.23 ( 3) link_NAG-ASN : angle 1.21101 / 0.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 SER cc_start: 0.7616 (p) cc_final: 0.7412 (p) REVERT: A 310 MET cc_start: 0.6403 (mmm) cc_final: 0.5579 (mmm) REVERT: A 315 ILE cc_start: 0.8191 (pt) cc_final: 0.7657 (mt) REVERT: A 334 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7069 (mmt180) REVERT: A 392 PHE cc_start: 0.7850 (t80) cc_final: 0.7558 (t80) REVERT: A 449 MET cc_start: 0.7119 (mmm) cc_final: 0.6908 (mmm) outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 0.0548 time to fit residues: 5.7804 Evaluate side-chains 75 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 50.0000 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 3 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.210425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.164827 restraints weight = 6651.028| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.96 r_work: 0.3843 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5204 Z= 0.129 Angle : 0.526 8.663 7091 Z= 0.264 Chirality : 0.041 0.241 814 Planarity : 0.004 0.042 880 Dihedral : 10.764 83.496 978 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.92 % Allowed : 20.67 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.33), residues: 664 helix: 1.71 (0.28), residues: 352 sheet: 0.81 (0.64), residues: 66 loop : -1.11 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.011 0.001 TYR A 306 PHE 0.012 0.001 PHE A 707 TRP 0.012 0.001 TRP A 320 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 5197) covalent geometry : angle 0.51331 / 0.26 ( 7070) hydrogen bonds : bond 0.04303 / 2.76 ( 301) hydrogen bonds : angle 4.11085 / 2.95 ( 885) link_BETA1-4 : bond 0.00551 / 0.27 ( 4) link_BETA1-4 : angle 2.67958 / 1.83 ( 12) link_NAG-ASN : bond 0.00416 / 0.20 ( 3) link_NAG-ASN : angle 1.04274 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.7078 (mtp85) REVERT: A 310 MET cc_start: 0.6374 (mmm) cc_final: 0.5730 (mmt) REVERT: A 315 ILE cc_start: 0.8078 (pt) cc_final: 0.7862 (pt) REVERT: A 392 PHE cc_start: 0.7825 (t80) cc_final: 0.7511 (t80) REVERT: A 449 MET cc_start: 0.7073 (mmm) cc_final: 0.6805 (mmm) REVERT: A 450 MET cc_start: 0.7984 (tpp) cc_final: 0.7107 (tpp) REVERT: A 716 ILE cc_start: 0.7827 (mm) cc_final: 0.7618 (pt) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.0579 time to fit residues: 5.8270 Evaluate side-chains 73 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 552 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 54 optimal weight: 0.0170 chunk 65 optimal weight: 8.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.214167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.167677 restraints weight = 6751.763| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.20 r_work: 0.3881 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5204 Z= 0.124 Angle : 0.517 8.539 7091 Z= 0.260 Chirality : 0.040 0.213 814 Planarity : 0.003 0.040 880 Dihedral : 9.851 84.946 978 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.25 % Allowed : 20.67 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.33), residues: 664 helix: 1.76 (0.28), residues: 355 sheet: 1.12 (0.63), residues: 66 loop : -1.07 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.010 0.001 TYR A 212 PHE 0.012 0.001 PHE A 245 TRP 0.013 0.001 TRP A 320 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 5197) covalent geometry : angle 0.50736 / 0.26 ( 7070) hydrogen bonds : bond 0.04214 / 2.72 ( 301) hydrogen bonds : angle 4.05039 / 2.90 ( 885) link_BETA1-4 : bond 0.00532 / 0.26 ( 4) link_BETA1-4 : angle 2.39542 / 1.60 ( 12) link_NAG-ASN : bond 0.00425 / 0.21 ( 3) link_NAG-ASN : angle 0.95713 / 0.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.6394 (mmm) cc_final: 0.5635 (mmm) REVERT: A 315 ILE cc_start: 0.8126 (pt) cc_final: 0.7904 (pt) REVERT: A 392 PHE cc_start: 0.7836 (t80) cc_final: 0.7530 (t80) REVERT: A 458 SER cc_start: 0.7816 (p) cc_final: 0.7433 (m) outliers start: 10 outliers final: 10 residues processed: 75 average time/residue: 0.0540 time to fit residues: 5.6024 Evaluate side-chains 76 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 chunk 29 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.213832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.168380 restraints weight = 6649.952| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.06 r_work: 0.3899 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5204 Z= 0.119 Angle : 0.497 7.924 7091 Z= 0.252 Chirality : 0.040 0.161 814 Planarity : 0.003 0.040 880 Dihedral : 9.030 74.749 978 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.70 % Allowed : 20.67 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.33), residues: 664 helix: 1.76 (0.28), residues: 357 sheet: 0.92 (0.66), residues: 59 loop : -0.85 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.009 0.001 TYR A 212 PHE 0.013 0.001 PHE A 245 TRP 0.009 0.001 TRP A 320 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 5197) covalent geometry : angle 0.48951 / 0.25 ( 7070) hydrogen bonds : bond 0.04082 / 2.61 ( 301) hydrogen bonds : angle 3.97557 / 2.85 ( 885) link_BETA1-4 : bond 0.00598 / 0.29 ( 4) link_BETA1-4 : angle 2.09417 / 1.38 ( 12) link_NAG-ASN : bond 0.00383 / 0.19 ( 3) link_NAG-ASN : angle 0.91480 / 0.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.7784 (tt) cc_final: 0.7463 (tp) REVERT: A 310 MET cc_start: 0.6389 (mmm) cc_final: 0.5677 (mmm) REVERT: A 315 ILE cc_start: 0.8162 (pt) cc_final: 0.7946 (pt) REVERT: A 334 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7019 (mpt180) REVERT: A 392 PHE cc_start: 0.7854 (t80) cc_final: 0.7599 (t80) REVERT: A 458 SER cc_start: 0.7776 (p) cc_final: 0.7430 (m) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.0560 time to fit residues: 5.9372 Evaluate side-chains 78 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 20 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.211392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166166 restraints weight = 6637.108| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.94 r_work: 0.3853 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5204 Z= 0.155 Angle : 0.521 7.172 7091 Z= 0.265 Chirality : 0.041 0.154 814 Planarity : 0.003 0.038 880 Dihedral : 8.554 72.688 978 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.92 % Allowed : 20.67 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.33), residues: 664 helix: 1.66 (0.27), residues: 355 sheet: 1.14 (0.65), residues: 59 loop : -0.93 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 624 TYR 0.013 0.001 TYR A 306 PHE 0.017 0.001 PHE A 439 TRP 0.013 0.001 TRP A 320 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5197) covalent geometry : angle 0.51496 / 0.26 ( 7070) hydrogen bonds : bond 0.04601 / 2.94 ( 301) hydrogen bonds : angle 4.05980 / 2.91 ( 885) link_BETA1-4 : bond 0.00530 / 0.26 ( 4) link_BETA1-4 : angle 1.94524 / 1.28 ( 12) link_NAG-ASN : bond 0.00382 / 0.19 ( 3) link_NAG-ASN : angle 0.83828 / 0.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.7796 (tt) cc_final: 0.7518 (tp) REVERT: A 282 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: A 310 MET cc_start: 0.6377 (mmm) cc_final: 0.5780 (mmt) REVERT: A 315 ILE cc_start: 0.8171 (pt) cc_final: 0.7970 (pt) REVERT: A 334 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7099 (mpt180) REVERT: A 353 THR cc_start: 0.7702 (m) cc_final: 0.7124 (t) REVERT: A 392 PHE cc_start: 0.7884 (t80) cc_final: 0.7491 (t80) REVERT: A 450 MET cc_start: 0.8046 (tpp) cc_final: 0.7279 (tpp) REVERT: A 458 SER cc_start: 0.7803 (p) cc_final: 0.7432 (m) REVERT: A 725 LEU cc_start: 0.8161 (tp) cc_final: 0.7819 (tt) outliers start: 13 outliers final: 9 residues processed: 78 average time/residue: 0.0785 time to fit residues: 7.9805 Evaluate side-chains 80 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 40.0000 chunk 52 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 56 optimal weight: 50.0000 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.210468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.164581 restraints weight = 6612.809| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.02 r_work: 0.3798 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5204 Z= 0.181 Angle : 0.545 7.699 7091 Z= 0.277 Chirality : 0.042 0.153 814 Planarity : 0.003 0.037 880 Dihedral : 8.252 70.582 978 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.25 % Allowed : 21.80 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.33), residues: 664 helix: 1.45 (0.27), residues: 354 sheet: 1.12 (0.64), residues: 59 loop : -0.95 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.015 0.002 TYR A 306 PHE 0.019 0.001 PHE A 439 TRP 0.013 0.002 TRP A 320 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 5197) covalent geometry : angle 0.53928 / 0.28 ( 7070) hydrogen bonds : bond 0.04867 / 3.14 ( 301) hydrogen bonds : angle 4.16326 / 2.99 ( 885) link_BETA1-4 : bond 0.00490 / 0.24 ( 4) link_BETA1-4 : angle 1.83268 / 1.22 ( 12) link_NAG-ASN : bond 0.00380 / 0.19 ( 3) link_NAG-ASN : angle 0.81906 / 0.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 156 LEU cc_start: 0.7673 (tt) cc_final: 0.7381 (tp) REVERT: A 282 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: A 310 MET cc_start: 0.6351 (mmm) cc_final: 0.5769 (mmt) REVERT: A 315 ILE cc_start: 0.8218 (pt) cc_final: 0.8000 (pt) REVERT: A 334 ARG cc_start: 0.7674 (mtp85) cc_final: 0.7102 (mpt180) REVERT: A 353 THR cc_start: 0.7689 (m) cc_final: 0.7101 (t) REVERT: A 392 PHE cc_start: 0.7897 (t80) cc_final: 0.7518 (t80) REVERT: A 450 MET cc_start: 0.8049 (tpp) cc_final: 0.7761 (tpp) REVERT: A 458 SER cc_start: 0.7850 (p) cc_final: 0.7441 (m) REVERT: A 626 ARG cc_start: 0.6572 (ptm160) cc_final: 0.5966 (ptm160) REVERT: A 725 LEU cc_start: 0.8026 (tp) cc_final: 0.7783 (tt) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.0703 time to fit residues: 6.9524 Evaluate side-chains 77 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.4980 chunk 43 optimal weight: 0.0980 chunk 59 optimal weight: 50.0000 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.211445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.166143 restraints weight = 6657.527| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.97 r_work: 0.3783 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5204 Z= 0.142 Angle : 0.508 6.602 7091 Z= 0.261 Chirality : 0.040 0.154 814 Planarity : 0.003 0.038 880 Dihedral : 7.987 66.997 978 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.70 % Allowed : 21.57 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.33), residues: 664 helix: 1.54 (0.27), residues: 355 sheet: 0.94 (0.63), residues: 65 loop : -0.88 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 624 TYR 0.011 0.001 TYR A 306 PHE 0.014 0.001 PHE A 439 TRP 0.012 0.001 TRP A 320 HIS 0.002 0.000 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 5197) covalent geometry : angle 0.50328 / 0.26 ( 7070) hydrogen bonds : bond 0.04470 / 2.86 ( 301) hydrogen bonds : angle 4.06208 / 2.91 ( 885) link_BETA1-4 : bond 0.00443 / 0.22 ( 4) link_BETA1-4 : angle 1.71990 / 1.16 ( 12) link_NAG-ASN : bond 0.00373 / 0.18 ( 3) link_NAG-ASN : angle 0.73158 / 0.39 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7180 (tp) REVERT: A 282 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: A 310 MET cc_start: 0.6330 (mmm) cc_final: 0.5719 (mmt) REVERT: A 315 ILE cc_start: 0.8155 (pt) cc_final: 0.7938 (pt) REVERT: A 334 ARG cc_start: 0.7615 (mtp85) cc_final: 0.6980 (mpt180) REVERT: A 353 THR cc_start: 0.7651 (m) cc_final: 0.7059 (t) REVERT: A 450 MET cc_start: 0.7999 (tpp) cc_final: 0.7209 (tpp) REVERT: A 725 LEU cc_start: 0.7952 (tp) cc_final: 0.7708 (tt) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.0669 time to fit residues: 6.6095 Evaluate side-chains 78 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 40.0000 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 chunk 33 optimal weight: 0.0570 chunk 17 optimal weight: 0.0060 chunk 52 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.2632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.211734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166852 restraints weight = 6713.237| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.98 r_work: 0.3877 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5204 Z= 0.124 Angle : 0.516 9.873 7091 Z= 0.259 Chirality : 0.040 0.153 814 Planarity : 0.003 0.039 880 Dihedral : 7.813 62.722 978 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.80 % Allowed : 22.25 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.33), residues: 664 helix: 1.62 (0.27), residues: 356 sheet: 1.04 (0.63), residues: 65 loop : -0.80 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 359 TYR 0.010 0.001 TYR A 212 PHE 0.011 0.001 PHE A 245 TRP 0.012 0.001 TRP A 295 HIS 0.002 0.000 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 5197) covalent geometry : angle 0.51226 / 0.26 ( 7070) hydrogen bonds : bond 0.04237 / 2.72 ( 301) hydrogen bonds : angle 3.99960 / 2.85 ( 885) link_BETA1-4 : bond 0.00415 / 0.20 ( 4) link_BETA1-4 : angle 1.62191 / 1.11 ( 12) link_NAG-ASN : bond 0.00365 / 0.18 ( 3) link_NAG-ASN : angle 0.69010 / 0.37 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1830.18 seconds wall clock time: 31 minutes 49.75 seconds (1909.75 seconds total)