Starting phenix.real_space_refine on Fri Jul 19 13:27:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tny_41429/07_2024/8tny_41429.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tny_41429/07_2024/8tny_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tny_41429/07_2024/8tny_41429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tny_41429/07_2024/8tny_41429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tny_41429/07_2024/8tny_41429.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tny_41429/07_2024/8tny_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 Residue "B GLU 60": "OE1" <-> "OE2" Residue "B TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.44, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 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: 0.89 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: 2.48 Time building geometry restraints manager: 3.60 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: 95.35 - 103.07: 52 103.07 - 110.79: 2889 110.79 - 118.50: 3731 118.50 - 126.22: 4388 126.22 - 133.94: 96 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 2.440 nonbonded pdb=" OG1 THR A 226 " pdb=" O PHE A 434 " model vdw 2.118 2.440 nonbonded pdb=" O LEU B 122 " pdb=" OG SER B 126 " model vdw 2.241 2.440 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 126 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR A 142 " pdb=" O THR A 366 " model vdw 2.267 2.440 ... (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 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: 3.050 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.480 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- 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= 0.392 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 *********************** 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 fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 0.860 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: 0.1611 time to fit residues: 59.6108 Evaluate side-chains 187 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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: 0.5980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 415 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 415 ASN A 547 GLN A 573 GLN A 680 GLN A 696 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8184 Z= 0.205 Angle : 0.598 8.246 11156 Z= 0.300 Chirality : 0.041 0.171 1390 Planarity : 0.004 0.030 1360 Dihedral : 5.735 45.699 1174 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 8.46 % Allowed : 29.29 % 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: 1.43 (0.26), residues: 1066 helix: 1.88 (0.19), residues: 724 sheet: -1.55 (0.55), residues: 64 loop : -0.89 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 515 HIS 0.003 0.001 HIS A 647 PHE 0.016 0.002 PHE A 227 TYR 0.009 0.001 TYR B 271 ARG 0.001 0.000 ARG A 492 *********************** 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 260 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 191 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 431 PHE cc_start: 0.8648 (m-10) cc_final: 0.8398 (m-80) REVERT: B 504 MET cc_start: 0.6437 (mtp) cc_final: 0.5948 (mtp) REVERT: A 153 LEU cc_start: 0.7623 (mm) cc_final: 0.7420 (mt) REVERT: A 431 PHE cc_start: 0.8653 (m-10) cc_final: 0.8401 (m-80) REVERT: A 504 MET cc_start: 0.6434 (mtp) cc_final: 0.5944 (mtp) outliers start: 69 outliers final: 37 residues processed: 228 average time/residue: 0.1306 time to fit residues: 44.9799 Evaluate side-chains 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 231 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 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 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 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 231 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 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 467 VAL Chi-restraints excluded: chain A residue 511 ASP 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 680 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 0.0030 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 573 GLN B 680 GLN A 159 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 573 GLN A 680 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2478 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= 0.204 Angle : 0.560 8.288 11156 Z= 0.285 Chirality : 0.041 0.150 1390 Planarity : 0.004 0.031 1360 Dihedral : 3.977 31.536 1152 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.62 % Allowed : 32.11 % Favored : 61.27 % 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: 1.63 (0.26), residues: 1066 helix: 2.01 (0.19), residues: 724 sheet: -1.32 (0.58), residues: 64 loop : -0.79 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 515 HIS 0.002 0.000 HIS A 647 PHE 0.019 0.002 PHE A 152 TYR 0.009 0.001 TYR B 151 ARG 0.001 0.000 ARG B 545 *********************** 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 239 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 185 time to evaluate : 0.905 Fit side-chains REVERT: B 431 PHE cc_start: 0.8686 (m-10) cc_final: 0.8415 (m-80) REVERT: B 504 MET cc_start: 0.6567 (mtp) cc_final: 0.6020 (mtp) REVERT: B 580 ILE cc_start: 0.9174 (mp) cc_final: 0.8936 (mt) REVERT: A 431 PHE cc_start: 0.8709 (m-10) cc_final: 0.8446 (m-80) REVERT: A 504 MET cc_start: 0.6549 (mtp) cc_final: 0.6005 (mtp) REVERT: A 580 ILE cc_start: 0.9174 (mp) cc_final: 0.8936 (mt) outliers start: 54 outliers final: 33 residues processed: 213 average time/residue: 0.1274 time to fit residues: 41.3727 Evaluate side-chains 208 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain B residue 162 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 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 611 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 SER 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 298 HIS Chi-restraints excluded: chain A residue 373 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8184 Z= 0.209 Angle : 0.564 10.234 11156 Z= 0.287 Chirality : 0.040 0.152 1390 Planarity : 0.004 0.032 1360 Dihedral : 3.822 27.428 1148 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 7.23 % Allowed : 31.50 % Favored : 61.27 % 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: 1.68 (0.26), residues: 1066 helix: 2.06 (0.19), residues: 718 sheet: -0.71 (0.64), residues: 52 loop : -0.92 (0.38), residues: 296 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 0.020 0.002 PHE A 152 TYR 0.010 0.001 TYR B 151 ARG 0.002 0.000 ARG B 545 *********************** 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 234 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 175 time to evaluate : 0.903 Fit side-chains REVERT: B 275 LEU cc_start: 0.7609 (tp) cc_final: 0.7293 (mm) REVERT: B 431 PHE cc_start: 0.8727 (m-10) cc_final: 0.8463 (m-80) REVERT: B 504 MET cc_start: 0.6595 (mtp) cc_final: 0.6286 (mtm) REVERT: A 275 LEU cc_start: 0.7613 (tp) cc_final: 0.7296 (mm) REVERT: A 431 PHE cc_start: 0.8713 (m-10) cc_final: 0.8444 (m-80) REVERT: A 442 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7057 (mttp) REVERT: A 504 MET cc_start: 0.6586 (mtp) cc_final: 0.6279 (mtm) outliers start: 59 outliers final: 42 residues processed: 202 average time/residue: 0.1304 time to fit residues: 40.2728 Evaluate side-chains 208 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 220 MET 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 360 ILE 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 533 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 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 156 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 360 ILE 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 442 LYS 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8184 Z= 0.192 Angle : 0.550 11.538 11156 Z= 0.276 Chirality : 0.040 0.149 1390 Planarity : 0.003 0.034 1360 Dihedral : 3.683 24.812 1147 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.99 % Allowed : 32.84 % Favored : 60.17 % 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: 1.71 (0.27), residues: 1066 helix: 2.10 (0.20), residues: 712 sheet: -0.61 (0.65), residues: 52 loop : -0.92 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 290 HIS 0.001 0.000 HIS B 408 PHE 0.017 0.001 PHE A 152 TYR 0.010 0.001 TYR B 419 ARG 0.002 0.000 ARG B 545 *********************** 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 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 166 time to evaluate : 0.864 Fit side-chains REVERT: B 431 PHE cc_start: 0.8705 (m-10) cc_final: 0.8432 (m-80) REVERT: A 431 PHE cc_start: 0.8705 (m-10) cc_final: 0.8445 (m-80) REVERT: A 442 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7148 (mttp) outliers start: 57 outliers final: 34 residues processed: 191 average time/residue: 0.1278 time to fit residues: 37.8218 Evaluate side-chains 195 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET 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 588 TYR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 611 VAL 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 220 MET 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 442 LYS 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 588 TYR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 611 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 A 159 HIS A 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3221 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= 0.213 Angle : 0.558 11.145 11156 Z= 0.279 Chirality : 0.040 0.150 1390 Planarity : 0.004 0.034 1360 Dihedral : 3.566 17.300 1146 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 7.35 % Allowed : 31.37 % Favored : 61.27 % 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: 1.73 (0.27), residues: 1066 helix: 2.11 (0.20), residues: 712 sheet: -0.45 (0.69), residues: 52 loop : -0.92 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 290 HIS 0.001 0.001 HIS B 408 PHE 0.015 0.001 PHE A 152 TYR 0.011 0.001 TYR A 139 ARG 0.002 0.000 ARG B 545 *********************** 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 224 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 164 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: B 431 PHE cc_start: 0.8717 (m-10) cc_final: 0.8470 (m-80) REVERT: B 442 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7181 (mttp) REVERT: B 504 MET cc_start: 0.6920 (mtm) cc_final: 0.6609 (mtp) REVERT: A 136 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: A 431 PHE cc_start: 0.8711 (m-10) cc_final: 0.8465 (m-80) REVERT: A 442 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7221 (mttp) REVERT: A 504 MET cc_start: 0.6911 (mtm) cc_final: 0.6606 (mtp) outliers start: 60 outliers final: 44 residues processed: 193 average time/residue: 0.1227 time to fit residues: 36.5872 Evaluate side-chains 206 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 136 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 363 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 442 LYS 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 481 SER 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 590 ILE Chi-restraints excluded: chain B residue 611 VAL 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 231 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 363 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 442 LYS 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 481 SER 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 590 ILE Chi-restraints excluded: chain A residue 611 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3393 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= 0.182 Angle : 0.541 8.481 11156 Z= 0.272 Chirality : 0.040 0.147 1390 Planarity : 0.003 0.034 1360 Dihedral : 3.564 17.668 1146 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.50 % Allowed : 32.72 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.91 (0.27), residues: 1066 helix: 2.22 (0.20), residues: 704 sheet: -0.00 (0.72), residues: 52 loop : -0.77 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 515 HIS 0.002 0.000 HIS B 408 PHE 0.014 0.001 PHE A 152 TYR 0.015 0.001 TYR A 139 ARG 0.001 0.000 ARG B 545 *********************** 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 219 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 166 time to evaluate : 0.830 Fit side-chains REVERT: B 418 MET cc_start: 0.8273 (tmm) cc_final: 0.7797 (tmm) REVERT: B 431 PHE cc_start: 0.8712 (m-10) cc_final: 0.8484 (m-80) REVERT: B 504 MET cc_start: 0.6938 (mtm) cc_final: 0.6611 (mtp) REVERT: B 580 ILE cc_start: 0.9123 (mp) cc_final: 0.8813 (mt) REVERT: A 418 MET cc_start: 0.8256 (tmm) cc_final: 0.7777 (tmm) REVERT: A 431 PHE cc_start: 0.8716 (m-10) cc_final: 0.8471 (m-80) REVERT: A 442 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7265 (mttp) REVERT: A 504 MET cc_start: 0.6932 (mtm) cc_final: 0.6613 (mtp) REVERT: A 580 ILE cc_start: 0.9123 (mp) cc_final: 0.8810 (mt) outliers start: 53 outliers final: 40 residues processed: 196 average time/residue: 0.1276 time to fit residues: 38.4598 Evaluate side-chains 201 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 176 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 481 SER 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 590 ILE Chi-restraints excluded: chain B residue 611 VAL 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 156 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 MET 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 442 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 481 SER 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 590 ILE Chi-restraints excluded: chain A residue 611 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3456 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= 0.232 Angle : 0.565 8.619 11156 Z= 0.286 Chirality : 0.041 0.153 1390 Planarity : 0.004 0.035 1360 Dihedral : 3.553 16.891 1146 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.50 % Allowed : 33.33 % Favored : 60.17 % 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: 1.78 (0.27), residues: 1066 helix: 2.07 (0.20), residues: 718 sheet: 0.08 (0.71), residues: 52 loop : -0.85 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 515 HIS 0.001 0.000 HIS B 408 PHE 0.019 0.002 PHE A 152 TYR 0.033 0.001 TYR B 139 ARG 0.002 0.000 ARG B 545 *********************** 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 207 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 154 time to evaluate : 0.897 Fit side-chains REVERT: B 136 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: B 418 MET cc_start: 0.8202 (tmm) cc_final: 0.7787 (tmm) REVERT: B 431 PHE cc_start: 0.8716 (m-10) cc_final: 0.8502 (m-10) REVERT: B 442 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7188 (mttp) REVERT: B 504 MET cc_start: 0.6967 (mtm) cc_final: 0.6629 (mtp) REVERT: A 418 MET cc_start: 0.8198 (tmm) cc_final: 0.7784 (tmm) REVERT: A 431 PHE cc_start: 0.8739 (m-10) cc_final: 0.8520 (m-80) REVERT: A 442 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7291 (mttp) REVERT: A 504 MET cc_start: 0.6956 (mtm) cc_final: 0.6625 (mtp) outliers start: 53 outliers final: 44 residues processed: 188 average time/residue: 0.1351 time to fit residues: 38.4971 Evaluate side-chains 200 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 153 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 136 GLU 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 298 HIS Chi-restraints excluded: chain B residue 363 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 442 LYS 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 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 590 ILE Chi-restraints excluded: chain B residue 611 VAL 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 156 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 363 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 442 LYS 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 562 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.0040 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8184 Z= 0.191 Angle : 0.558 8.669 11156 Z= 0.279 Chirality : 0.041 0.188 1390 Planarity : 0.003 0.035 1360 Dihedral : 3.524 17.173 1146 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.51 % Allowed : 34.19 % Favored : 60.29 % 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: 1.93 (0.27), residues: 1066 helix: 2.22 (0.20), residues: 704 sheet: 0.43 (0.74), residues: 48 loop : -0.78 (0.38), residues: 314 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 0.016 0.001 PHE A 152 TYR 0.022 0.001 TYR B 139 ARG 0.001 0.000 ARG B 53 *********************** 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 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 0.877 Fit side-chains REVERT: B 136 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: B 418 MET cc_start: 0.8218 (tmm) cc_final: 0.7814 (tmm) REVERT: B 431 PHE cc_start: 0.8716 (m-10) cc_final: 0.8497 (m-10) REVERT: B 442 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7178 (mttp) REVERT: B 504 MET cc_start: 0.6931 (mtm) cc_final: 0.6595 (mtp) REVERT: A 418 MET cc_start: 0.8215 (tmm) cc_final: 0.7814 (tmm) REVERT: A 431 PHE cc_start: 0.8730 (m-10) cc_final: 0.8516 (m-80) REVERT: A 442 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7280 (mttp) REVERT: A 504 MET cc_start: 0.6921 (mtm) cc_final: 0.6596 (mtp) outliers start: 45 outliers final: 39 residues processed: 182 average time/residue: 0.1334 time to fit residues: 37.0778 Evaluate side-chains 196 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 136 GLU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET 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 442 LYS 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 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 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 156 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 MET 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 442 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 481 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8184 Z= 0.261 Angle : 0.588 8.234 11156 Z= 0.299 Chirality : 0.042 0.167 1390 Planarity : 0.004 0.034 1360 Dihedral : 3.605 15.753 1146 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.76 % Allowed : 34.31 % Favored : 59.93 % 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: 2.03 (0.20), residues: 718 sheet: 0.09 (0.70), residues: 48 loop : -0.77 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 515 HIS 0.003 0.001 HIS B 292 PHE 0.015 0.002 PHE B 394 TYR 0.023 0.002 TYR B 139 ARG 0.001 0.000 ARG B 545 ********************** 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 205 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 0.892 Fit side-chains REVERT: B 136 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 161 SER cc_start: 0.8029 (t) cc_final: 0.7797 (t) REVERT: B 418 MET cc_start: 0.8205 (tmm) cc_final: 0.7804 (tmm) REVERT: B 431 PHE cc_start: 0.8802 (m-10) cc_final: 0.8593 (m-10) REVERT: B 442 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7196 (mttp) REVERT: B 504 MET cc_start: 0.6983 (mtm) cc_final: 0.6627 (mtp) REVERT: A 418 MET cc_start: 0.8199 (tmm) cc_final: 0.7789 (tmm) REVERT: A 442 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7259 (mttp) REVERT: A 466 LEU cc_start: 0.8420 (mm) cc_final: 0.7904 (tp) REVERT: A 504 MET cc_start: 0.6980 (mtm) cc_final: 0.6631 (mtp) outliers start: 47 outliers final: 40 residues processed: 186 average time/residue: 0.1368 time to fit residues: 38.5671 Evaluate side-chains 198 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 155 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 363 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 442 LYS 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 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 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 162 VAL Chi-restraints excluded: chain A residue 220 MET 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 442 LYS 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 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 A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.160047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127795 restraints weight = 12604.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131735 restraints weight = 6666.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134118 restraints weight = 4540.308| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8184 Z= 0.193 Angle : 0.563 8.763 11156 Z= 0.283 Chirality : 0.041 0.164 1390 Planarity : 0.003 0.035 1360 Dihedral : 3.566 17.399 1146 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.64 % Allowed : 34.56 % Favored : 59.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 1066 helix: 2.07 (0.20), residues: 716 sheet: 0.35 (0.72), residues: 48 loop : -0.87 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 515 HIS 0.003 0.000 HIS A 292 PHE 0.015 0.001 PHE A 152 TYR 0.022 0.001 TYR B 139 ARG 0.002 0.000 ARG B 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1783.58 seconds wall clock time: 32 minutes 43.45 seconds (1963.45 seconds total)