Starting phenix.real_space_refine on Sun May 11 13:25:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tny_41429/05_2025/8tny_41429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tny_41429/05_2025/8tny_41429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tny_41429/05_2025/8tny_41429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tny_41429/05_2025/8tny_41429.map" model { file = "/net/cci-nas-00/data/ceres_data/8tny_41429/05_2025/8tny_41429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tny_41429/05_2025/8tny_41429.cif" } resolution = 3.55 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= 0.002 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5258 2.51 5 N 1316 2.21 5 O 1408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8026 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4008 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 17, 'TRANS': 527} Chain breaks: 5 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 119 Chain: "A" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4008 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 17, 'TRANS': 527} Chain breaks: 5 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.71 Number of scatterers: 8026 At special positions: 0 Unit cell: (118.118, 65.254, 96.642, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1408 8.00 N 1316 7.00 C 5258 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: 2.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 70.8% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.604A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 4.043A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 154 removed outlier: 3.899A pdb=" N GLY B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 214 through 240 Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.619A pdb=" N VAL B 244 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 247 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 273 removed outlier: 4.167A pdb=" N LYS B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'B' and resid 335 through 351 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 378 through 408 removed outlier: 4.961A pdb=" N VAL B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.748A pdb=" N HIS B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'B' and resid 455 through 470 removed outlier: 3.645A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 479 through 496 removed outlier: 3.877A pdb=" N LEU B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'B' and resid 508 through 524 removed outlier: 3.522A pdb=" N THR B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 548 removed outlier: 3.500A pdb=" N ILE B 543 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 603 Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'B' and resid 660 through 678 Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.586A pdb=" N ASN B 724 " --> pdb=" O GLU B 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.604A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.043A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.899A pdb=" N GLY A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 214 through 240 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.619A pdb=" N VAL A 244 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A 247 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 273 removed outlier: 4.167A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 378 through 408 removed outlier: 4.961A pdb=" N VAL A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.748A pdb=" N HIS A 432 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.645A pdb=" N VAL A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 479 through 496 removed outlier: 3.877A pdb=" N LEU A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 508 through 524 removed outlier: 3.522A pdb=" N THR A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 548 removed outlier: 3.501A pdb=" N ILE A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 603 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 660 through 678 Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.586A pdb=" N ASN A 724 " --> pdb=" O GLU A 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AA2, first strand: chain 'B' and resid 563 through 565 removed outlier: 4.779A pdb=" N ILE B 580 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N LEU B 556 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 13.115A pdb=" N ILE B 578 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 579 " --> pdb=" O VAL B 650 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP B 652 " --> pdb=" O LYS B 579 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 581 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N PHE B 709 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU B 683 " --> pdb=" O PHE B 709 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 563 through 565 removed outlier: 4.779A pdb=" N ILE A 580 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N LEU A 556 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 13.115A pdb=" N ILE A 578 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS A 579 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP A 652 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 581 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N PHE A 709 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 683 " --> pdb=" O PHE A 709 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1584 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: 2.51 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1294 1.32 - 1.44: 2126 1.44 - 1.57: 4704 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 8184 Sorted by residual: bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.536 1.444 0.091 1.65e-02 3.67e+03 3.06e+01 bond pdb=" CA SER B 126 " pdb=" CB SER B 126 " ideal model delta sigma weight residual 1.536 1.444 0.091 1.65e-02 3.67e+03 3.06e+01 bond pdb=" O4 SO4 A 801 " pdb=" S SO4 A 801 " ideal model delta sigma weight residual 1.499 1.430 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O4 SO4 B 801 " pdb=" S SO4 B 801 " ideal model delta sigma weight residual 1.499 1.430 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O3 SO4 B 801 " pdb=" S SO4 B 801 " ideal model delta sigma weight residual 1.499 1.431 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 8179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 10696 2.09 - 4.18: 402 4.18 - 6.27: 40 6.27 - 8.35: 8 8.35 - 10.44: 10 Bond angle restraints: 11156 Sorted by residual: angle pdb=" CA ILE B 120 " pdb=" C ILE B 120 " pdb=" N LEU B 121 " ideal model delta sigma weight residual 118.56 111.90 6.66 9.90e-01 1.02e+00 4.53e+01 angle pdb=" CA ILE A 120 " pdb=" C ILE A 120 " pdb=" N LEU A 121 " ideal model delta sigma weight residual 118.56 111.90 6.66 9.90e-01 1.02e+00 4.53e+01 angle pdb=" C GLN A 547 " pdb=" CA GLN A 547 " pdb=" CB GLN A 547 " ideal model delta sigma weight residual 110.79 101.63 9.16 1.66e+00 3.63e-01 3.04e+01 angle pdb=" C GLN B 547 " pdb=" CA GLN B 547 " pdb=" CB GLN B 547 " ideal model delta sigma weight residual 110.79 101.63 9.16 1.66e+00 3.63e-01 3.04e+01 angle pdb=" N PRO A 549 " pdb=" CD PRO A 549 " pdb=" CG PRO A 549 " ideal model delta sigma weight residual 103.20 95.35 7.85 1.50e+00 4.44e-01 2.74e+01 ... (remaining 11151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 4022 15.98 - 31.95: 500 31.95 - 47.93: 176 47.93 - 63.91: 66 63.91 - 79.88: 14 Dihedral angle restraints: 4778 sinusoidal: 1618 harmonic: 3160 Sorted by residual: dihedral pdb=" C GLN A 547 " pdb=" N GLN A 547 " pdb=" CA GLN A 547 " pdb=" CB GLN A 547 " ideal model delta harmonic sigma weight residual -122.60 -113.08 -9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C GLN B 547 " pdb=" N GLN B 547 " pdb=" CA GLN B 547 " pdb=" CB GLN B 547 " ideal model delta harmonic sigma weight residual -122.60 -113.08 -9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C TYR A 129 " pdb=" N TYR A 129 " pdb=" CA TYR A 129 " pdb=" CB TYR A 129 " ideal model delta harmonic sigma weight residual -122.60 -131.51 8.91 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 4775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1024 0.050 - 0.100: 262 0.100 - 0.151: 66 0.151 - 0.201: 32 0.201 - 0.251: 6 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA ILE A 164 " pdb=" N ILE A 164 " pdb=" C ILE A 164 " pdb=" CB ILE A 164 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ILE B 164 " pdb=" N ILE B 164 " pdb=" C ILE B 164 " pdb=" CB ILE B 164 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LYS A 548 " pdb=" N LYS A 548 " pdb=" C LYS A 548 " pdb=" CB LYS A 548 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1387 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 120 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ILE A 120 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE A 120 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 121 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 120 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ILE B 120 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE B 120 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU B 121 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 548 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C LYS B 548 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS B 548 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 549 " 0.013 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 156 2.67 - 3.23: 8355 3.23 - 3.79: 12938 3.79 - 4.34: 16351 4.34 - 4.90: 27075 Nonbonded interactions: 64875 Sorted by model distance: nonbonded pdb=" OG1 THR B 226 " pdb=" O PHE B 434 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR A 226 " pdb=" O PHE A 434 " model vdw 2.118 3.040 nonbonded pdb=" O LEU B 122 " pdb=" OG SER B 126 " model vdw 2.241 3.040 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 126 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR A 142 " pdb=" O THR A 366 " model vdw 2.267 3.040 ... (remaining 64870 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.290 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.091 8184 Z= 0.386 Angle : 0.857 10.443 11156 Z= 0.566 Chirality : 0.055 0.251 1390 Planarity : 0.005 0.046 1360 Dihedral : 17.953 79.881 2734 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.25 % Favored : 94.56 % Rotamer: Outliers : 5.02 % Allowed : 32.97 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 1066 helix: 1.54 (0.20), residues: 718 sheet: -1.34 (0.62), residues: 64 loop : -1.18 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 376 HIS 0.002 0.001 HIS A 647 PHE 0.013 0.001 PHE A 368 TYR 0.018 0.002 TYR A 139 ARG 0.001 0.000 ARG B 582 Details of bonding type rmsd hydrogen bonds : bond 0.14107 ( 546) hydrogen bonds : angle 5.73169 ( 1584) covalent geometry : bond 0.00612 ( 8184) covalent geometry : angle 0.85735 (11156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.897 Fit side-chains REVERT: B 356 TYR cc_start: 0.6737 (t80) cc_final: 0.6384 (t80) REVERT: B 431 PHE cc_start: 0.8529 (m-10) cc_final: 0.8249 (m-10) REVERT: B 466 LEU cc_start: 0.8447 (mm) cc_final: 0.7966 (tp) REVERT: B 504 MET cc_start: 0.6848 (mtp) cc_final: 0.6349 (mtp) REVERT: B 548 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7726 (mttm) REVERT: A 356 TYR cc_start: 0.6732 (t80) cc_final: 0.6382 (t80) REVERT: A 431 PHE cc_start: 0.8527 (m-10) cc_final: 0.8248 (m-10) REVERT: A 466 LEU cc_start: 0.8444 (mm) cc_final: 0.7962 (tp) REVERT: A 504 MET cc_start: 0.6852 (mtp) cc_final: 0.6351 (mtp) REVERT: A 548 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7725 (mttm) outliers start: 41 outliers final: 12 residues processed: 261 average time/residue: 0.1622 time to fit residues: 60.1602 Evaluate side-chains 187 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 548 LYS Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 548 LYS Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 268 GLN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 547 GLN B 573 GLN B 680 GLN B 696 ASN A 159 HIS A 268 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 547 GLN A 573 GLN A 680 GLN A 696 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124326 restraints weight = 12471.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128392 restraints weight = 6651.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131035 restraints weight = 4511.390| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8184 Z= 0.154 Angle : 0.619 8.064 11156 Z= 0.313 Chirality : 0.042 0.168 1390 Planarity : 0.004 0.030 1360 Dihedral : 5.944 51.060 1174 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 8.70 % Allowed : 29.29 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1066 helix: 1.85 (0.19), residues: 724 sheet: -1.54 (0.55), residues: 64 loop : -0.94 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 515 HIS 0.004 0.001 HIS A 647 PHE 0.016 0.002 PHE B 368 TYR 0.011 0.001 TYR A 247 ARG 0.001 0.000 ARG B 671 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 546) hydrogen bonds : angle 4.24829 ( 1584) covalent geometry : bond 0.00360 ( 8184) covalent geometry : angle 0.61897 (11156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 188 time to evaluate : 0.841 Fit side-chains REVERT: B 153 LEU cc_start: 0.7688 (mm) cc_final: 0.7486 (mt) REVERT: B 431 PHE cc_start: 0.8666 (m-10) cc_final: 0.8434 (m-10) REVERT: B 442 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7684 (mttp) REVERT: B 504 MET cc_start: 0.6560 (mtp) cc_final: 0.6067 (mtp) REVERT: A 153 LEU cc_start: 0.7683 (mm) cc_final: 0.7470 (mt) REVERT: A 431 PHE cc_start: 0.8675 (m-10) cc_final: 0.8442 (m-10) REVERT: A 442 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7628 (mttp) REVERT: A 504 MET cc_start: 0.6553 (mtp) cc_final: 0.6066 (mtp) outliers start: 71 outliers final: 36 residues processed: 229 average time/residue: 0.1367 time to fit residues: 47.0381 Evaluate side-chains 207 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 680 GLN Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 680 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 8.9990 chunk 67 optimal weight: 0.0770 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 353 HIS B 573 GLN B 680 GLN A 159 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 353 HIS A 573 GLN A 680 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.165878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133078 restraints weight = 12676.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137200 restraints weight = 6750.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.139832 restraints weight = 4585.942| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8184 Z= 0.140 Angle : 0.577 7.719 11156 Z= 0.298 Chirality : 0.042 0.151 1390 Planarity : 0.004 0.030 1360 Dihedral : 4.479 42.760 1160 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 7.60 % Allowed : 29.17 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1066 helix: 1.97 (0.19), residues: 724 sheet: -1.44 (0.58), residues: 64 loop : -0.81 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 515 HIS 0.002 0.001 HIS A 647 PHE 0.020 0.002 PHE A 152 TYR 0.012 0.001 TYR A 139 ARG 0.002 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 546) hydrogen bonds : angle 4.01465 ( 1584) covalent geometry : bond 0.00331 ( 8184) covalent geometry : angle 0.57733 (11156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 176 time to evaluate : 0.899 Fit side-chains REVERT: B 153 LEU cc_start: 0.7689 (mm) cc_final: 0.7488 (mt) REVERT: B 179 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8086 (tp30) REVERT: B 431 PHE cc_start: 0.8587 (m-10) cc_final: 0.8330 (m-10) REVERT: B 504 MET cc_start: 0.6644 (mtp) cc_final: 0.6136 (mtp) REVERT: B 580 ILE cc_start: 0.9248 (mp) cc_final: 0.8995 (mt) REVERT: B 707 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 153 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7483 (mt) REVERT: A 179 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8088 (tp30) REVERT: A 431 PHE cc_start: 0.8622 (m-10) cc_final: 0.8365 (m-10) REVERT: A 504 MET cc_start: 0.6636 (mtp) cc_final: 0.6138 (mtp) REVERT: A 580 ILE cc_start: 0.9244 (mp) cc_final: 0.8992 (mt) REVERT: A 707 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8415 (mt) outliers start: 62 outliers final: 37 residues processed: 212 average time/residue: 0.1398 time to fit residues: 45.4291 Evaluate side-chains 206 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 301 ASN B 573 GLN B 680 GLN A 159 HIS A 301 ASN A 573 GLN A 680 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132654 restraints weight = 12548.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136779 restraints weight = 6644.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139364 restraints weight = 4490.909| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 0.044 8184 Z= 0.131 Angle : 0.573 10.695 11156 Z= 0.291 Chirality : 0.041 0.148 1390 Planarity : 0.004 0.032 1360 Dihedral : 3.929 28.135 1148 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 7.11 % Allowed : 29.29 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.27), residues: 1066 helix: 2.05 (0.19), residues: 724 sheet: -1.22 (0.60), residues: 64 loop : -0.67 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 515 HIS 0.002 0.001 HIS B 353 PHE 0.020 0.001 PHE A 152 TYR 0.011 0.001 TYR B 151 ARG 0.002 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 546) hydrogen bonds : angle 3.87115 ( 1584) covalent geometry : bond 0.00306 ( 8184) covalent geometry : angle 0.57311 (11156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.987 Fit side-chains REVERT: B 179 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8057 (tp30) REVERT: B 275 LEU cc_start: 0.7737 (tp) cc_final: 0.7424 (mm) REVERT: B 431 PHE cc_start: 0.8565 (m-10) cc_final: 0.8309 (m-10) REVERT: B 504 MET cc_start: 0.6593 (mtp) cc_final: 0.6297 (mtm) REVERT: B 707 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8460 (mt) REVERT: A 179 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8047 (tp30) REVERT: A 275 LEU cc_start: 0.7737 (tp) cc_final: 0.7425 (mm) REVERT: A 431 PHE cc_start: 0.8598 (m-10) cc_final: 0.8311 (m-80) REVERT: A 504 MET cc_start: 0.6590 (mtp) cc_final: 0.6295 (mtm) REVERT: A 707 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8459 (mt) outliers start: 58 outliers final: 44 residues processed: 201 average time/residue: 0.1327 time to fit residues: 40.9911 Evaluate side-chains 205 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 680 GLN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 0.0010 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 680 GLN A 159 HIS A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.164054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131217 restraints weight = 12476.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135177 restraints weight = 6678.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137633 restraints weight = 4572.921| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8184 Z= 0.150 Angle : 0.583 10.661 11156 Z= 0.294 Chirality : 0.041 0.147 1390 Planarity : 0.004 0.032 1360 Dihedral : 3.805 25.620 1147 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 8.33 % Allowed : 29.17 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.27), residues: 1066 helix: 2.02 (0.19), residues: 724 sheet: -0.53 (0.69), residues: 52 loop : -0.79 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 515 HIS 0.001 0.001 HIS A 353 PHE 0.017 0.002 PHE A 152 TYR 0.011 0.001 TYR B 139 ARG 0.002 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 546) hydrogen bonds : angle 3.85089 ( 1584) covalent geometry : bond 0.00362 ( 8184) covalent geometry : angle 0.58319 (11156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 161 time to evaluate : 0.914 Fit side-chains REVERT: B 179 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8057 (tp30) REVERT: B 275 LEU cc_start: 0.7740 (tp) cc_final: 0.7433 (mm) REVERT: B 286 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8039 (tp) REVERT: B 431 PHE cc_start: 0.8589 (m-10) cc_final: 0.8320 (m-10) REVERT: A 179 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8059 (tp30) REVERT: A 275 LEU cc_start: 0.7733 (tp) cc_final: 0.7426 (mm) REVERT: A 286 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8044 (tp) REVERT: A 431 PHE cc_start: 0.8616 (m-10) cc_final: 0.8328 (m-10) outliers start: 68 outliers final: 45 residues processed: 198 average time/residue: 0.1255 time to fit residues: 38.5383 Evaluate side-chains 207 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 48 optimal weight: 0.0370 chunk 89 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 680 GLN A 159 HIS A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.164559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131812 restraints weight = 12448.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135867 restraints weight = 6632.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138442 restraints weight = 4501.312| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8184 Z= 0.132 Angle : 0.575 8.124 11156 Z= 0.287 Chirality : 0.041 0.147 1390 Planarity : 0.003 0.034 1360 Dihedral : 3.699 23.501 1146 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 7.35 % Allowed : 28.80 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.27), residues: 1066 helix: 2.06 (0.19), residues: 720 sheet: -0.19 (0.70), residues: 52 loop : -0.85 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 515 HIS 0.002 0.001 HIS B 408 PHE 0.017 0.001 PHE A 152 TYR 0.010 0.001 TYR B 151 ARG 0.001 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 546) hydrogen bonds : angle 3.76448 ( 1584) covalent geometry : bond 0.00309 ( 8184) covalent geometry : angle 0.57469 (11156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 1.003 Fit side-chains REVERT: B 431 PHE cc_start: 0.8589 (m-10) cc_final: 0.8351 (m-10) REVERT: B 504 MET cc_start: 0.6928 (mtm) cc_final: 0.6661 (mtp) REVERT: B 580 ILE cc_start: 0.9223 (mp) cc_final: 0.8928 (mt) REVERT: A 431 PHE cc_start: 0.8603 (m-10) cc_final: 0.8342 (m-10) REVERT: A 504 MET cc_start: 0.6922 (mtm) cc_final: 0.6667 (mtp) REVERT: A 580 ILE cc_start: 0.9222 (mp) cc_final: 0.8930 (mt) outliers start: 60 outliers final: 47 residues processed: 195 average time/residue: 0.1289 time to fit residues: 39.3161 Evaluate side-chains 210 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 680 GLN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 680 GLN A 159 HIS A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.162140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128696 restraints weight = 12657.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132946 restraints weight = 6477.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135606 restraints weight = 4279.295| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8184 Z= 0.123 Angle : 0.568 8.330 11156 Z= 0.284 Chirality : 0.040 0.145 1390 Planarity : 0.003 0.034 1360 Dihedral : 3.680 23.460 1146 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 7.48 % Allowed : 29.41 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.27), residues: 1066 helix: 2.08 (0.20), residues: 718 sheet: -0.08 (0.72), residues: 52 loop : -0.88 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 515 HIS 0.001 0.000 HIS B 408 PHE 0.014 0.001 PHE A 152 TYR 0.013 0.001 TYR B 139 ARG 0.001 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 546) hydrogen bonds : angle 3.78967 ( 1584) covalent geometry : bond 0.00290 ( 8184) covalent geometry : angle 0.56819 (11156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 161 time to evaluate : 0.930 Fit side-chains REVERT: B 431 PHE cc_start: 0.8587 (m-10) cc_final: 0.8341 (m-10) REVERT: B 504 MET cc_start: 0.6995 (mtm) cc_final: 0.6702 (mtp) REVERT: A 136 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: A 431 PHE cc_start: 0.8589 (m-10) cc_final: 0.8339 (m-10) REVERT: A 504 MET cc_start: 0.6998 (mtm) cc_final: 0.6711 (mtp) outliers start: 61 outliers final: 49 residues processed: 192 average time/residue: 0.1255 time to fit residues: 37.1074 Evaluate side-chains 204 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 680 GLN Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 680 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 82 optimal weight: 0.0040 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 680 GLN A 159 HIS A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.160477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127386 restraints weight = 12753.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131342 restraints weight = 6708.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133854 restraints weight = 4559.549| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8184 Z= 0.148 Angle : 0.576 7.873 11156 Z= 0.291 Chirality : 0.041 0.146 1390 Planarity : 0.004 0.034 1360 Dihedral : 3.658 20.083 1146 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 7.48 % Allowed : 30.27 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 1066 helix: 2.08 (0.19), residues: 720 sheet: -0.19 (0.72), residues: 52 loop : -0.83 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 515 HIS 0.001 0.001 HIS B 408 PHE 0.013 0.001 PHE B 394 TYR 0.012 0.001 TYR A 139 ARG 0.001 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 546) hydrogen bonds : angle 3.81643 ( 1584) covalent geometry : bond 0.00356 ( 8184) covalent geometry : angle 0.57572 (11156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 154 time to evaluate : 0.902 Fit side-chains REVERT: B 431 PHE cc_start: 0.8644 (m-10) cc_final: 0.8405 (m-10) REVERT: B 504 MET cc_start: 0.7023 (mtm) cc_final: 0.6709 (mtp) REVERT: A 136 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: A 431 PHE cc_start: 0.8574 (m-10) cc_final: 0.8360 (m-10) REVERT: A 504 MET cc_start: 0.7032 (mtm) cc_final: 0.6726 (mtp) outliers start: 61 outliers final: 54 residues processed: 186 average time/residue: 0.1234 time to fit residues: 35.9390 Evaluate side-chains 207 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 680 GLN Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 680 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 680 GLN A 159 HIS A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.161565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128027 restraints weight = 12818.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132237 restraints weight = 6513.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134896 restraints weight = 4320.332| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8184 Z= 0.125 Angle : 0.583 8.187 11156 Z= 0.290 Chirality : 0.041 0.151 1390 Planarity : 0.004 0.034 1360 Dihedral : 3.646 18.929 1146 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 7.11 % Allowed : 30.27 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.27), residues: 1066 helix: 2.11 (0.20), residues: 718 sheet: 0.05 (0.73), residues: 48 loop : -0.89 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 515 HIS 0.002 0.000 HIS A 292 PHE 0.012 0.001 PHE B 394 TYR 0.011 0.001 TYR B 139 ARG 0.001 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 546) hydrogen bonds : angle 3.80935 ( 1584) covalent geometry : bond 0.00294 ( 8184) covalent geometry : angle 0.58328 (11156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 0.927 Fit side-chains REVERT: B 431 PHE cc_start: 0.8661 (m-10) cc_final: 0.8428 (m-10) REVERT: B 504 MET cc_start: 0.6996 (mtm) cc_final: 0.6667 (mtp) REVERT: B 580 ILE cc_start: 0.9224 (mp) cc_final: 0.8941 (mt) REVERT: A 136 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 431 PHE cc_start: 0.8563 (m-10) cc_final: 0.8325 (m-80) REVERT: A 504 MET cc_start: 0.6997 (mtm) cc_final: 0.6676 (mtp) REVERT: A 580 ILE cc_start: 0.9222 (mp) cc_final: 0.8941 (mt) outliers start: 58 outliers final: 51 residues processed: 181 average time/residue: 0.1268 time to fit residues: 36.0822 Evaluate side-chains 194 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 680 GLN Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 680 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 36 optimal weight: 0.0770 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 680 GLN A 159 HIS A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.161022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127439 restraints weight = 12625.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131596 restraints weight = 6460.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134266 restraints weight = 4305.216| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8184 Z= 0.137 Angle : 0.579 7.962 11156 Z= 0.291 Chirality : 0.041 0.147 1390 Planarity : 0.004 0.034 1360 Dihedral : 3.633 17.219 1146 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.86 % Allowed : 30.76 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.27), residues: 1066 helix: 2.07 (0.20), residues: 716 sheet: 0.09 (0.73), residues: 48 loop : -0.88 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 515 HIS 0.002 0.001 HIS B 292 PHE 0.016 0.001 PHE B 152 TYR 0.011 0.001 TYR B 139 ARG 0.001 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 546) hydrogen bonds : angle 3.82862 ( 1584) covalent geometry : bond 0.00329 ( 8184) covalent geometry : angle 0.57904 (11156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 0.842 Fit side-chains REVERT: B 302 LEU cc_start: 0.7816 (tp) cc_final: 0.7563 (mm) REVERT: B 431 PHE cc_start: 0.8659 (m-10) cc_final: 0.8430 (m-10) REVERT: B 504 MET cc_start: 0.7028 (mtm) cc_final: 0.6710 (mtp) REVERT: B 580 ILE cc_start: 0.9231 (mp) cc_final: 0.8943 (mt) REVERT: A 136 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: A 302 LEU cc_start: 0.7790 (tp) cc_final: 0.7542 (mm) REVERT: A 431 PHE cc_start: 0.8642 (m-10) cc_final: 0.8434 (m-80) REVERT: A 504 MET cc_start: 0.7036 (mtm) cc_final: 0.6724 (mtp) REVERT: A 580 ILE cc_start: 0.9229 (mp) cc_final: 0.8942 (mt) outliers start: 56 outliers final: 49 residues processed: 177 average time/residue: 0.1193 time to fit residues: 33.0886 Evaluate side-chains 195 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 588 TYR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 648 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 680 GLN A 159 HIS A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.161113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127358 restraints weight = 12589.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131514 restraints weight = 6458.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134148 restraints weight = 4320.508| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8184 Z= 0.133 Angle : 0.582 7.855 11156 Z= 0.294 Chirality : 0.041 0.144 1390 Planarity : 0.004 0.036 1360 Dihedral : 3.621 17.221 1146 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.13 % Allowed : 31.25 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 1066 helix: 2.08 (0.20), residues: 716 sheet: 0.22 (0.76), residues: 48 loop : -0.86 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 515 HIS 0.001 0.001 HIS B 408 PHE 0.013 0.001 PHE B 394 TYR 0.017 0.001 TYR B 142 ARG 0.001 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 546) hydrogen bonds : angle 3.82401 ( 1584) covalent geometry : bond 0.00319 ( 8184) covalent geometry : angle 0.58170 (11156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2647.02 seconds wall clock time: 47 minutes 10.92 seconds (2830.92 seconds total)