Starting phenix.real_space_refine on Thu Mar 13 00:02:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgf_31967/03_2025/7vgf_31967.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgf_31967/03_2025/7vgf_31967.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/7vgf_31967/03_2025/7vgf_31967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgf_31967/03_2025/7vgf_31967.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgf_31967/03_2025/7vgf_31967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgf_31967/03_2025/7vgf_31967.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 5284 2.51 5 N 1412 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8280 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4108 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 13, 'TRANS': 536} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4108 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 13, 'TRANS': 536} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.22, per 1000 atoms: 0.63 Number of scatterers: 8280 At special positions: 0 Unit cell: (110.526, 67.938, 133.848, 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 20 16.00 P 6 15.00 Mg 2 11.99 O 1556 8.00 N 1412 7.00 C 5284 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 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 989.8 milliseconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 69.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 133 through 171 removed outlier: 3.642A pdb=" N ARG A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 186 through 234 Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.745A pdb=" N HIS A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 289 removed outlier: 4.163A pdb=" N LYS A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 290 through 339 removed outlier: 3.814A pdb=" N ALA A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 318 " --> pdb=" O TRP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 349 through 402 removed outlier: 3.870A pdb=" N ALA A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 removed outlier: 3.686A pdb=" N VAL A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 432 removed outlier: 3.668A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.560A pdb=" N LEU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'A' and resid 574 through 585 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 610 through 626 removed outlier: 3.647A pdb=" N LYS A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 656 removed outlier: 3.788A pdb=" N LYS A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.647A pdb=" N VAL A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'B' and resid 133 through 171 removed outlier: 3.642A pdb=" N ARG B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Proline residue: B 158 - end of helix Processing helix chain 'B' and resid 186 through 234 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.746A pdb=" N HIS B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 289 removed outlier: 4.163A pdb=" N LYS B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 290 through 339 removed outlier: 3.814A pdb=" N ALA B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 318 " --> pdb=" O TRP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 349 through 402 removed outlier: 3.870A pdb=" N ALA B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 422 removed outlier: 3.686A pdb=" N VAL B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 removed outlier: 3.668A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 450 Processing helix chain 'B' and resid 512 through 519 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.559A pdb=" N LEU B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 574 through 585 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 610 through 626 removed outlier: 3.648A pdb=" N LYS B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 656 removed outlier: 3.789A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.646A pdb=" N VAL B 670 " --> pdb=" O ARG B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 693 Processing sheet with id=AA1, first strand: chain 'A' and resid 488 through 491 removed outlier: 5.702A pdb=" N VAL A 477 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 477 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS A 526 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 548 through 551 removed outlier: 6.489A pdb=" N VAL A 501 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS A 500 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE A 677 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 502 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 679 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 504 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 686 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP A 680 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 561 Processing sheet with id=AA4, first strand: chain 'B' and resid 488 through 491 removed outlier: 5.703A pdb=" N VAL B 477 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 477 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS B 526 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 548 through 551 removed outlier: 6.489A pdb=" N VAL B 501 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS B 500 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE B 677 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 502 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 679 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 504 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 686 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 680 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 560 through 561 610 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 2.67 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: 2690 1.34 - 1.46: 1056 1.46 - 1.57: 4627 1.57 - 1.69: 8 1.69 - 1.81: 41 Bond restraints: 8422 Sorted by residual: bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.609 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C4 ANP A 901 " pdb=" C5 ANP A 901 " ideal model delta sigma weight residual 1.387 1.471 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" N3B ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.669 1.750 -0.081 2.00e-02 2.50e+03 1.66e+01 ... (remaining 8417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 11358 3.29 - 6.59: 87 6.59 - 9.88: 15 9.88 - 13.17: 1 13.17 - 16.46: 1 Bond angle restraints: 11462 Sorted by residual: angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 110.49 16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" N GLU B 604 " pdb=" CA GLU B 604 " pdb=" C GLU B 604 " ideal model delta sigma weight residual 111.07 106.69 4.38 1.07e+00 8.73e-01 1.68e+01 angle pdb=" N GLU A 604 " pdb=" CA GLU A 604 " pdb=" C GLU A 604 " ideal model delta sigma weight residual 111.07 106.71 4.36 1.07e+00 8.73e-01 1.66e+01 angle pdb=" N VAL A 450 " pdb=" CA VAL A 450 " pdb=" C VAL A 450 " ideal model delta sigma weight residual 112.98 108.30 4.68 1.25e+00 6.40e-01 1.40e+01 angle pdb=" N VAL B 450 " pdb=" CA VAL B 450 " pdb=" C VAL B 450 " ideal model delta sigma weight residual 112.98 108.33 4.65 1.25e+00 6.40e-01 1.38e+01 ... (remaining 11457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.29: 4665 22.29 - 44.58: 279 44.58 - 66.87: 33 66.87 - 89.16: 12 89.16 - 111.45: 1 Dihedral angle restraints: 4990 sinusoidal: 1836 harmonic: 3154 Sorted by residual: dihedral pdb=" O1A ANP A 901 " pdb=" O3A ANP A 901 " pdb=" PA ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sinusoidal sigma weight residual 83.11 -165.44 -111.45 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" CA ARG A 520 " pdb=" C ARG A 520 " pdb=" N PHE A 521 " pdb=" CA PHE A 521 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ARG B 520 " pdb=" C ARG B 520 " pdb=" N PHE B 521 " pdb=" CA PHE B 521 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1118 0.050 - 0.100: 225 0.100 - 0.151: 28 0.151 - 0.201: 2 0.201 - 0.251: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" C2' ANP A 901 " pdb=" C1' ANP A 901 " pdb=" C3' ANP A 901 " pdb=" O2' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.72 -2.55 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1371 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 466 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 467 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 467 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 467 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 466 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 467 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 222 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE B 222 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE B 222 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG B 223 " -0.009 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 97 2.65 - 3.21: 8143 3.21 - 3.77: 12822 3.77 - 4.34: 16458 4.34 - 4.90: 27071 Nonbonded interactions: 64591 Sorted by model distance: nonbonded pdb=" OG SER B 512 " pdb="MG MG B 902 " model vdw 2.083 2.170 nonbonded pdb=" OG SER A 512 " pdb="MG MG A 902 " model vdw 2.084 2.170 nonbonded pdb=" O1G ANP B 901 " pdb="MG MG B 902 " model vdw 2.120 2.170 nonbonded pdb=" OG1 THR B 636 " pdb=" O2G ANP B 901 " model vdw 2.210 3.040 nonbonded pdb=" OG SER B 610 " pdb=" OE1 GLU B 613 " model vdw 2.259 3.040 ... (remaining 64586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.950 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.390 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.004 0.144 8422 Z= 0.293 Angle : 0.696 16.463 11462 Z= 0.346 Chirality : 0.040 0.251 1374 Planarity : 0.003 0.043 1456 Dihedral : 14.500 111.448 2970 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.26), residues: 1092 helix: 2.84 (0.19), residues: 724 sheet: 1.10 (0.67), residues: 54 loop : -0.91 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 314 HIS 0.002 0.000 HIS A 234 PHE 0.020 0.002 PHE B 214 TYR 0.009 0.001 TYR A 196 ARG 0.003 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8592 (tmmt) cc_final: 0.7919 (ttmm) REVERT: A 559 HIS cc_start: 0.7897 (t-90) cc_final: 0.7455 (t-90) REVERT: B 225 ILE cc_start: 0.8485 (mp) cc_final: 0.8270 (mp) REVERT: B 260 ILE cc_start: 0.7685 (mm) cc_final: 0.7458 (tt) REVERT: B 324 LYS cc_start: 0.8484 (tmmt) cc_final: 0.7915 (ttmt) REVERT: B 327 ASN cc_start: 0.8425 (t0) cc_final: 0.8142 (t0) REVERT: B 392 ILE cc_start: 0.8159 (tp) cc_final: 0.7817 (tt) REVERT: B 559 HIS cc_start: 0.7930 (t-90) cc_final: 0.7507 (t-90) REVERT: B 663 ILE cc_start: 0.7571 (mt) cc_final: 0.7331 (mt) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.2171 time to fit residues: 56.0428 Evaluate side-chains 130 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN B 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.168887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144642 restraints weight = 11686.410| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.00 r_work: 0.3730 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8422 Z= 0.180 Angle : 0.517 5.065 11462 Z= 0.273 Chirality : 0.039 0.134 1374 Planarity : 0.003 0.032 1456 Dihedral : 7.824 95.010 1250 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.43 % Allowed : 9.31 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.26), residues: 1092 helix: 2.98 (0.19), residues: 726 sheet: 1.56 (0.66), residues: 50 loop : -0.92 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 314 HIS 0.003 0.001 HIS A 657 PHE 0.015 0.001 PHE B 214 TYR 0.011 0.001 TYR B 196 ARG 0.005 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8227 (ttmm) REVERT: A 339 ASN cc_start: 0.7787 (m-40) cc_final: 0.7435 (m-40) REVERT: B 257 THR cc_start: 0.8634 (p) cc_final: 0.8430 (p) REVERT: B 260 ILE cc_start: 0.8257 (mm) cc_final: 0.8033 (tt) REVERT: B 324 LYS cc_start: 0.8635 (tmmt) cc_final: 0.8301 (ttmt) REVERT: B 327 ASN cc_start: 0.8790 (t0) cc_final: 0.8557 (t0) REVERT: B 392 ILE cc_start: 0.8551 (tp) cc_final: 0.8183 (tt) REVERT: B 633 ASP cc_start: 0.7876 (t0) cc_final: 0.7579 (m-30) outliers start: 12 outliers final: 9 residues processed: 138 average time/residue: 0.1775 time to fit residues: 35.2290 Evaluate side-chains 134 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140404 restraints weight = 11780.658| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.00 r_work: 0.3673 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8422 Z= 0.199 Angle : 0.503 5.197 11462 Z= 0.268 Chirality : 0.039 0.131 1374 Planarity : 0.003 0.026 1456 Dihedral : 6.966 80.775 1246 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 11.58 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.26), residues: 1092 helix: 2.98 (0.19), residues: 728 sheet: 1.60 (0.70), residues: 50 loop : -1.01 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS B 588 PHE 0.022 0.002 PHE A 385 TYR 0.011 0.001 TYR B 196 ARG 0.010 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.876 Fit side-chains REVERT: A 324 LYS cc_start: 0.8811 (tmmt) cc_final: 0.8375 (ttmm) REVERT: A 339 ASN cc_start: 0.7996 (m-40) cc_final: 0.7718 (m-40) REVERT: A 409 ASP cc_start: 0.8027 (t0) cc_final: 0.7737 (t0) REVERT: B 224 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7908 (mtm110) REVERT: B 324 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8138 (ttmm) REVERT: B 530 TYR cc_start: 0.6414 (m-80) cc_final: 0.6022 (m-10) outliers start: 19 outliers final: 16 residues processed: 145 average time/residue: 0.1739 time to fit residues: 36.5502 Evaluate side-chains 138 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 32 optimal weight: 0.0970 chunk 73 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 559 HIS ** 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 = 0.4039 r_free = 0.4039 target = 0.162605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138682 restraints weight = 11713.065| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.93 r_work: 0.3631 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8422 Z= 0.233 Angle : 0.533 9.329 11462 Z= 0.284 Chirality : 0.040 0.169 1374 Planarity : 0.003 0.023 1456 Dihedral : 7.079 77.865 1246 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.98 % Allowed : 13.96 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.26), residues: 1092 helix: 2.85 (0.19), residues: 724 sheet: 1.54 (0.72), residues: 50 loop : -1.16 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.005 0.001 HIS B 588 PHE 0.016 0.002 PHE B 385 TYR 0.010 0.001 TYR B 196 ARG 0.003 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8790 (tmmt) cc_final: 0.8389 (ttmm) REVERT: A 335 ASP cc_start: 0.8662 (t0) cc_final: 0.8454 (t0) REVERT: A 339 ASN cc_start: 0.8129 (m-40) cc_final: 0.7743 (m110) REVERT: A 345 TYR cc_start: 0.9000 (m-80) cc_final: 0.8778 (m-80) REVERT: B 324 LYS cc_start: 0.8701 (tmmt) cc_final: 0.8221 (ttmm) REVERT: B 530 TYR cc_start: 0.6514 (m-80) cc_final: 0.6140 (m-10) REVERT: B 663 ILE cc_start: 0.8165 (mt) cc_final: 0.7889 (mt) outliers start: 25 outliers final: 20 residues processed: 142 average time/residue: 0.1702 time to fit residues: 35.1270 Evaluate side-chains 146 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 100 optimal weight: 0.0570 chunk 9 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 559 HIS ** 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 = 0.4055 r_free = 0.4055 target = 0.163808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138954 restraints weight = 11662.763| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.00 r_work: 0.3635 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8422 Z= 0.187 Angle : 0.517 8.639 11462 Z= 0.278 Chirality : 0.040 0.191 1374 Planarity : 0.003 0.022 1456 Dihedral : 7.040 72.960 1246 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.34 % Allowed : 15.75 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.26), residues: 1092 helix: 2.89 (0.19), residues: 726 sheet: 1.46 (0.72), residues: 50 loop : -1.03 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 314 HIS 0.004 0.001 HIS B 588 PHE 0.022 0.002 PHE B 418 TYR 0.009 0.001 TYR A 196 ARG 0.005 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.082 Fit side-chains REVERT: A 324 LYS cc_start: 0.8770 (tmmt) cc_final: 0.8412 (ttmm) REVERT: A 339 ASN cc_start: 0.7996 (m-40) cc_final: 0.7622 (m110) REVERT: A 615 GLN cc_start: 0.8397 (mm110) cc_final: 0.7999 (mm110) REVERT: B 324 LYS cc_start: 0.8669 (tmmt) cc_final: 0.8224 (ttmm) REVERT: B 530 TYR cc_start: 0.6449 (m-80) cc_final: 0.6111 (m-10) REVERT: B 559 HIS cc_start: 0.8256 (t-90) cc_final: 0.8043 (t-90) REVERT: B 663 ILE cc_start: 0.8095 (mt) cc_final: 0.7791 (mt) outliers start: 28 outliers final: 22 residues processed: 143 average time/residue: 0.1630 time to fit residues: 34.6314 Evaluate side-chains 146 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 559 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138407 restraints weight = 11762.326| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.01 r_work: 0.3627 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8422 Z= 0.196 Angle : 0.523 7.966 11462 Z= 0.281 Chirality : 0.040 0.201 1374 Planarity : 0.003 0.022 1456 Dihedral : 6.893 69.341 1246 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.70 % Allowed : 15.63 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.26), residues: 1092 helix: 2.87 (0.19), residues: 726 sheet: 1.40 (0.73), residues: 50 loop : -0.97 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 314 HIS 0.004 0.001 HIS B 588 PHE 0.017 0.001 PHE B 418 TYR 0.022 0.001 TYR A 345 ARG 0.003 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.850 Fit side-chains REVERT: A 324 LYS cc_start: 0.8747 (tmmt) cc_final: 0.8384 (ttmm) REVERT: A 339 ASN cc_start: 0.7991 (m-40) cc_final: 0.7621 (m110) REVERT: A 345 TYR cc_start: 0.8655 (m-80) cc_final: 0.8327 (m-80) REVERT: A 427 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6786 (tt) REVERT: B 279 MET cc_start: 0.8466 (mmt) cc_final: 0.8244 (ttp) REVERT: B 324 LYS cc_start: 0.8694 (tmmt) cc_final: 0.8250 (ttmm) REVERT: B 427 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6822 (tt) REVERT: B 530 TYR cc_start: 0.6486 (m-80) cc_final: 0.6126 (m-10) REVERT: B 663 ILE cc_start: 0.8119 (mt) cc_final: 0.7799 (mt) outliers start: 31 outliers final: 26 residues processed: 141 average time/residue: 0.1519 time to fit residues: 32.0104 Evaluate side-chains 155 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133178 restraints weight = 11784.572| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.00 r_work: 0.3580 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8422 Z= 0.287 Angle : 0.585 7.861 11462 Z= 0.315 Chirality : 0.042 0.198 1374 Planarity : 0.003 0.026 1456 Dihedral : 7.054 63.932 1246 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.06 % Allowed : 16.23 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.26), residues: 1092 helix: 2.67 (0.19), residues: 720 sheet: 1.31 (0.75), residues: 50 loop : -1.18 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 314 HIS 0.007 0.001 HIS B 588 PHE 0.023 0.002 PHE A 262 TYR 0.027 0.002 TYR A 345 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.925 Fit side-chains REVERT: A 324 LYS cc_start: 0.8838 (tmmt) cc_final: 0.8508 (ttmm) REVERT: A 339 ASN cc_start: 0.8203 (m-40) cc_final: 0.7835 (m110) REVERT: A 345 TYR cc_start: 0.8998 (m-80) cc_final: 0.8745 (m-80) REVERT: A 427 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7083 (tt) REVERT: B 324 LYS cc_start: 0.8722 (tmmt) cc_final: 0.8320 (ttmm) REVERT: B 427 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6951 (tp) REVERT: B 530 TYR cc_start: 0.6622 (m-80) cc_final: 0.6245 (m-80) REVERT: B 663 ILE cc_start: 0.8162 (mt) cc_final: 0.7841 (mt) outliers start: 34 outliers final: 25 residues processed: 148 average time/residue: 0.1559 time to fit residues: 34.5511 Evaluate side-chains 153 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.160923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136570 restraints weight = 11803.658| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.96 r_work: 0.3629 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8422 Z= 0.197 Angle : 0.539 7.622 11462 Z= 0.285 Chirality : 0.040 0.201 1374 Planarity : 0.003 0.025 1456 Dihedral : 6.881 61.455 1246 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.18 % Allowed : 17.54 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.26), residues: 1092 helix: 2.83 (0.19), residues: 722 sheet: 1.23 (0.75), residues: 50 loop : -1.08 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 314 HIS 0.004 0.001 HIS B 588 PHE 0.013 0.001 PHE A 214 TYR 0.021 0.001 TYR A 345 ARG 0.005 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.886 Fit side-chains REVERT: A 324 LYS cc_start: 0.8807 (tmmt) cc_final: 0.8488 (ttmm) REVERT: A 339 ASN cc_start: 0.7956 (m-40) cc_final: 0.7651 (m110) REVERT: A 345 TYR cc_start: 0.8941 (m-80) cc_final: 0.8619 (m-80) REVERT: A 427 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6913 (tp) REVERT: B 324 LYS cc_start: 0.8683 (tmmt) cc_final: 0.8269 (ttmm) REVERT: B 427 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6982 (tt) REVERT: B 530 TYR cc_start: 0.6590 (m-80) cc_final: 0.6262 (m-10) REVERT: B 663 ILE cc_start: 0.8194 (mt) cc_final: 0.7855 (mt) outliers start: 35 outliers final: 30 residues processed: 141 average time/residue: 0.1714 time to fit residues: 36.2670 Evaluate side-chains 158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.161958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137324 restraints weight = 11906.945| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.01 r_work: 0.3606 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8422 Z= 0.179 Angle : 0.525 8.459 11462 Z= 0.277 Chirality : 0.040 0.217 1374 Planarity : 0.003 0.025 1456 Dihedral : 6.743 56.861 1246 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.18 % Allowed : 17.66 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.26), residues: 1092 helix: 2.91 (0.19), residues: 722 sheet: 1.22 (0.75), residues: 50 loop : -1.05 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 314 HIS 0.004 0.001 HIS B 588 PHE 0.013 0.001 PHE A 214 TYR 0.019 0.001 TYR A 345 ARG 0.003 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.926 Fit side-chains REVERT: A 324 LYS cc_start: 0.8779 (tmmt) cc_final: 0.8458 (ttmm) REVERT: A 339 ASN cc_start: 0.7960 (m-40) cc_final: 0.7606 (m110) REVERT: A 345 TYR cc_start: 0.8933 (m-80) cc_final: 0.8611 (m-80) REVERT: A 427 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6790 (tp) REVERT: B 324 LYS cc_start: 0.8658 (tmmt) cc_final: 0.8237 (ttmm) REVERT: B 427 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6892 (tt) REVERT: B 530 TYR cc_start: 0.6577 (m-80) cc_final: 0.6225 (m-10) REVERT: B 663 ILE cc_start: 0.8187 (mt) cc_final: 0.7852 (mt) outliers start: 35 outliers final: 30 residues processed: 143 average time/residue: 0.1604 time to fit residues: 33.8773 Evaluate side-chains 158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 0.0050 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.160515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135824 restraints weight = 11807.986| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.96 r_work: 0.3598 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8422 Z= 0.221 Angle : 0.563 8.587 11462 Z= 0.298 Chirality : 0.041 0.212 1374 Planarity : 0.003 0.026 1456 Dihedral : 6.756 53.823 1246 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.82 % Allowed : 18.14 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.26), residues: 1092 helix: 2.87 (0.19), residues: 722 sheet: 1.27 (0.75), residues: 50 loop : -1.10 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 314 HIS 0.005 0.001 HIS B 588 PHE 0.014 0.002 PHE B 385 TYR 0.021 0.001 TYR A 345 ARG 0.004 0.000 ARG A 520 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.946 Fit side-chains REVERT: A 324 LYS cc_start: 0.8782 (tmmt) cc_final: 0.8475 (ttmm) REVERT: A 339 ASN cc_start: 0.7985 (m-40) cc_final: 0.7639 (m110) REVERT: A 345 TYR cc_start: 0.8941 (m-80) cc_final: 0.8631 (m-80) REVERT: A 427 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6963 (tp) REVERT: B 324 LYS cc_start: 0.8665 (tmmt) cc_final: 0.8272 (ttmm) REVERT: B 427 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7022 (tt) REVERT: B 530 TYR cc_start: 0.6597 (m-80) cc_final: 0.6219 (m-80) REVERT: B 663 ILE cc_start: 0.8190 (mt) cc_final: 0.7861 (mt) outliers start: 32 outliers final: 28 residues processed: 142 average time/residue: 0.1605 time to fit residues: 33.9969 Evaluate side-chains 159 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.162337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137557 restraints weight = 11831.501| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.02 r_work: 0.3608 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8422 Z= 0.180 Angle : 0.544 8.459 11462 Z= 0.286 Chirality : 0.040 0.224 1374 Planarity : 0.003 0.025 1456 Dihedral : 6.550 54.437 1246 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.22 % Allowed : 18.97 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.26), residues: 1092 helix: 2.96 (0.19), residues: 722 sheet: 1.26 (0.75), residues: 50 loop : -1.03 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 314 HIS 0.003 0.001 HIS B 588 PHE 0.013 0.001 PHE A 214 TYR 0.020 0.001 TYR A 345 ARG 0.005 0.000 ARG A 520 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.68 seconds wall clock time: 77 minutes 33.12 seconds (4653.12 seconds total)