Starting phenix.real_space_refine on Mon May 19 07:38:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qa6_18300/05_2025/8qa6_18300_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qa6_18300/05_2025/8qa6_18300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qa6_18300/05_2025/8qa6_18300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qa6_18300/05_2025/8qa6_18300.map" model { file = "/net/cci-nas-00/data/ceres_data/8qa6_18300/05_2025/8qa6_18300_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qa6_18300/05_2025/8qa6_18300_trim.cif" } resolution = 2.91 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= -0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 44 5.16 5 C 5826 2.51 5 N 1518 2.21 5 O 1696 1.98 5 H 8720 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 17808 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8797 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 31, 'TRANS': 521} Chain breaks: 2 Chain: "B" Number of atoms: 8797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8797 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 31, 'TRANS': 521} Chain breaks: 2 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'FAD': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'FAD': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {None: 2} Time building chain proxies: 9.36, per 1000 atoms: 0.53 Number of scatterers: 17808 At special positions: 0 Unit cell: (106.19, 116.522, 78.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 4 15.00 O 1696 8.00 N 1518 7.00 C 5826 6.00 H 8720 1.00 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: 5.29 Conformation dependent library (CDL) restraints added in 1.4 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 51.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 69 through 85 removed outlier: 3.971A pdb=" N ALA A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.626A pdb=" N ASP A 100 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.811A pdb=" N LEU A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.834A pdb=" N PHE A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.652A pdb=" N LEU A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 3.746A pdb=" N LYS A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 290 through 313 removed outlier: 3.891A pdb=" N SER A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.524A pdb=" N THR A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 removed outlier: 5.626A pdb=" N TYR A 404 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.990A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 467 through 477 Processing helix chain 'A' and resid 518 through 530 removed outlier: 3.767A pdb=" N LYS A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 533 No H-bonds generated for 'chain 'A' and resid 531 through 533' Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.531A pdb=" N PHE A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 631 through 644 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 69 through 85 removed outlier: 3.970A pdb=" N ALA B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.625A pdb=" N ASP B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 134 through 149 Processing helix chain 'B' and resid 174 through 187 removed outlier: 3.906A pdb=" N LEU B 178 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.836A pdb=" N PHE B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.649A pdb=" N LEU B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.768A pdb=" N LYS B 281 " --> pdb=" O PRO B 277 " (cutoff:3.500A) Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 290 through 313 removed outlier: 3.870A pdb=" N SER B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 4.515A pdb=" N THR B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 removed outlier: 5.626A pdb=" N TYR B 404 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 407 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 427 through 441 removed outlier: 3.943A pdb=" N VAL B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 518 through 530 removed outlier: 3.762A pdb=" N LYS B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 533 No H-bonds generated for 'chain 'B' and resid 531 through 533' Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.534A pdb=" N PHE B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 599 Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'B' and resid 631 through 644 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 64 removed outlier: 3.585A pdb=" N HIS A 127 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 124 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N MET A 154 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 126 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS A 193 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 195 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 224 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 225 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY A 255 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 227 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLY A 317 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP A 59 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N PHE A 320 " --> pdb=" O TRP A 59 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER A 61 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 485 removed outlier: 6.505A pdb=" N GLU A 514 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 484 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR A 512 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.614A pdb=" N THR A 573 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP A 561 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A 571 " --> pdb=" O TRP A 561 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 64 removed outlier: 3.585A pdb=" N HIS B 127 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR B 124 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET B 154 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU B 126 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B 193 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA B 195 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 224 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 225 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY B 255 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 227 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLY B 317 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP B 59 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE B 320 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER B 61 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 480 through 485 removed outlier: 6.504A pdb=" N GLU B 514 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER B 484 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR B 512 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 506 through 509 removed outlier: 6.614A pdb=" N THR B 573 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP B 561 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN B 571 " --> pdb=" O TRP B 561 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1179 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: 6.62 Time building geometry restraints manager: 6.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8702 1.03 - 1.22: 18 1.22 - 1.42: 3990 1.42 - 1.62: 5266 1.62 - 1.81: 80 Bond restraints: 18056 Sorted by residual: bond pdb=" C2' SAM B 701 " pdb=" C3' SAM B 701 " ideal model delta sigma weight residual 1.532 1.247 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' SAM A 701 " pdb=" C3' SAM A 701 " ideal model delta sigma weight residual 1.532 1.247 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' SAM B 703 " pdb=" C3' SAM B 703 " ideal model delta sigma weight residual 1.532 1.251 0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C2' SAM A 703 " pdb=" C3' SAM A 703 " ideal model delta sigma weight residual 1.532 1.251 0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C6 SAM A 703 " pdb=" N6 SAM A 703 " ideal model delta sigma weight residual 1.333 1.456 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 18051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.49: 32521 5.49 - 10.98: 49 10.98 - 16.46: 10 16.46 - 21.95: 0 21.95 - 27.44: 8 Bond angle restraints: 32588 Sorted by residual: angle pdb=" C1' SAM B 703 " pdb=" N9 SAM B 703 " pdb=" C8 SAM B 703 " ideal model delta sigma weight residual 123.85 96.41 27.44 3.00e+00 1.11e-01 8.37e+01 angle pdb=" C1' SAM A 703 " pdb=" N9 SAM A 703 " pdb=" C8 SAM A 703 " ideal model delta sigma weight residual 123.85 96.45 27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" C1' SAM B 703 " pdb=" N9 SAM B 703 " pdb=" C4 SAM B 703 " ideal model delta sigma weight residual 130.15 156.71 -26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" C1' SAM A 703 " pdb=" N9 SAM A 703 " pdb=" C4 SAM A 703 " ideal model delta sigma weight residual 130.15 156.60 -26.45 3.00e+00 1.11e-01 7.78e+01 angle pdb=" C1' SAM B 701 " pdb=" N9 SAM B 701 " pdb=" C8 SAM B 701 " ideal model delta sigma weight residual 123.85 98.83 25.02 3.00e+00 1.11e-01 6.96e+01 ... (remaining 32583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 8233 34.91 - 69.81: 373 69.81 - 104.72: 34 104.72 - 139.62: 0 139.62 - 174.53: 2 Dihedral angle restraints: 8642 sinusoidal: 4752 harmonic: 3890 Sorted by residual: dihedral pdb=" O5' FAD A 702 " pdb=" O3P FAD A 702 " pdb=" P FAD A 702 " pdb=" PA FAD A 702 " ideal model delta sinusoidal sigma weight residual -61.77 112.76 -174.53 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5' FAD B 702 " pdb=" O3P FAD B 702 " pdb=" P FAD B 702 " pdb=" PA FAD B 702 " ideal model delta sinusoidal sigma weight residual -61.77 112.71 -174.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA ILE B 192 " pdb=" C ILE B 192 " pdb=" N CYS B 193 " pdb=" CA CYS B 193 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 8639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.323: 1360 0.323 - 0.646: 4 0.646 - 0.969: 0 0.969 - 1.292: 0 1.292 - 1.616: 4 Chirality restraints: 1368 Sorted by residual: chirality pdb=" SD SAM B 701 " pdb=" CG SAM B 701 " pdb=" CE SAM B 701 " pdb=" C5' SAM B 701 " both_signs ideal model delta sigma weight residual False 5.50 3.89 1.62 2.00e-01 2.50e+01 6.52e+01 chirality pdb=" SD SAM A 701 " pdb=" CG SAM A 701 " pdb=" CE SAM A 701 " pdb=" C5' SAM A 701 " both_signs ideal model delta sigma weight residual False 5.50 3.89 1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" SD SAM A 703 " pdb=" CG SAM A 703 " pdb=" CE SAM A 703 " pdb=" C5' SAM A 703 " both_signs ideal model delta sigma weight residual False 5.50 3.94 1.57 2.00e-01 2.50e+01 6.14e+01 ... (remaining 1365 not shown) Planarity restraints: 2646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 152 " 0.056 2.00e-02 2.50e+03 6.90e-02 7.14e+01 pdb=" CG ASN B 152 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 152 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 152 " -0.108 2.00e-02 2.50e+03 pdb="HD21 ASN B 152 " -0.006 2.00e-02 2.50e+03 pdb="HD22 ASN B 152 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 152 " -0.055 2.00e-02 2.50e+03 6.87e-02 7.08e+01 pdb=" CG ASN A 152 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 152 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 152 " 0.108 2.00e-02 2.50e+03 pdb="HD21 ASN A 152 " 0.006 2.00e-02 2.50e+03 pdb="HD22 ASN A 152 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 118 " -0.038 2.00e-02 2.50e+03 4.61e-02 3.19e+01 pdb=" CG ASN A 118 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 118 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 118 " 0.073 2.00e-02 2.50e+03 pdb="HD21 ASN A 118 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASN A 118 " -0.071 2.00e-02 2.50e+03 ... (remaining 2643 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 912 2.17 - 2.78: 34656 2.78 - 3.39: 51387 3.39 - 3.99: 66352 3.99 - 4.60: 103216 Nonbonded interactions: 256523 Sorted by model distance: nonbonded pdb=" OE1 GLU A 568 " pdb="HE22 GLN B 571 " model vdw 1.565 2.450 nonbonded pdb="HE22 GLN A 571 " pdb=" OE1 GLU B 568 " model vdw 1.566 2.450 nonbonded pdb="HE21 GLN A 555 " pdb=" H GLU B 568 " model vdw 1.605 2.100 nonbonded pdb=" HZ3 LYS B 584 " pdb=" OD1 ASP B 585 " model vdw 1.669 2.450 nonbonded pdb=" O VAL B 240 " pdb=" HG1 THR B 244 " model vdw 1.670 2.450 ... (remaining 256518 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: 0.05 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 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: 0.310 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 40.470 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.010 0.285 9336 Z= 0.500 Angle : 1.084 27.438 12696 Z= 0.428 Chirality : 0.098 1.616 1368 Planarity : 0.006 0.094 1608 Dihedral : 17.507 174.526 3576 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.52 % Allowed : 18.92 % Favored : 80.56 % 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: -0.54 (0.25), residues: 1094 helix: -0.01 (0.23), residues: 470 sheet: -0.08 (0.37), residues: 176 loop : -0.69 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 95 HIS 0.006 0.001 HIS B 181 PHE 0.021 0.001 PHE A 582 TYR 0.017 0.002 TYR B 90 ARG 0.009 0.001 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.14595 ( 413) hydrogen bonds : angle 7.21031 ( 1179) covalent geometry : bond 0.01013 ( 9336) covalent geometry : angle 1.08352 (12696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7861 (mmt) cc_final: 0.7466 (mmt) outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 1.9031 time to fit residues: 221.4297 Evaluate side-chains 106 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 TYR Chi-restraints excluded: chain B residue 119 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 477 GLN B 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124212 restraints weight = 32079.994| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.17 r_work: 0.3353 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9336 Z= 0.199 Angle : 0.620 5.866 12696 Z= 0.314 Chirality : 0.043 0.153 1368 Planarity : 0.005 0.039 1608 Dihedral : 11.345 176.319 1418 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.98 % Allowed : 17.67 % Favored : 80.35 % 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: 0.68 (0.26), residues: 1094 helix: 1.35 (0.24), residues: 476 sheet: -0.18 (0.38), residues: 178 loop : -0.15 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 95 HIS 0.004 0.001 HIS B 539 PHE 0.025 0.002 PHE B 582 TYR 0.013 0.002 TYR A 197 ARG 0.006 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 413) hydrogen bonds : angle 5.20775 ( 1179) covalent geometry : bond 0.00484 ( 9336) covalent geometry : angle 0.61978 (12696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7334 (mp0) REVERT: B 137 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6493 (mm-30) REVERT: B 399 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7348 (mp0) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 2.0315 time to fit residues: 261.6058 Evaluate side-chains 110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.154461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125101 restraints weight = 32072.964| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.11 r_work: 0.3364 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9336 Z= 0.140 Angle : 0.547 4.461 12696 Z= 0.277 Chirality : 0.041 0.147 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.788 170.535 1414 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.14 % Allowed : 18.30 % Favored : 80.56 % 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: 1.03 (0.26), residues: 1094 helix: 1.71 (0.24), residues: 476 sheet: -0.16 (0.38), residues: 178 loop : 0.03 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.007 0.001 HIS A 181 PHE 0.019 0.002 PHE A 582 TYR 0.012 0.001 TYR A 197 ARG 0.004 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 413) hydrogen bonds : angle 4.76583 ( 1179) covalent geometry : bond 0.00339 ( 9336) covalent geometry : angle 0.54671 (12696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7338 (mp0) REVERT: B 137 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6562 (mm-30) REVERT: B 399 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7357 (mp0) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 2.0277 time to fit residues: 254.4479 Evaluate side-chains 108 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN B 133 GLN B 477 GLN B 555 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121476 restraints weight = 32169.314| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.16 r_work: 0.3308 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9336 Z= 0.193 Angle : 0.581 4.527 12696 Z= 0.295 Chirality : 0.042 0.142 1368 Planarity : 0.004 0.039 1608 Dihedral : 10.983 165.928 1414 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.77 % Allowed : 18.40 % Favored : 79.83 % 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: 0.99 (0.26), residues: 1094 helix: 1.63 (0.24), residues: 476 sheet: -0.10 (0.39), residues: 174 loop : 0.01 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 95 HIS 0.005 0.001 HIS B 181 PHE 0.020 0.002 PHE A 582 TYR 0.013 0.002 TYR B 512 ARG 0.004 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 413) hydrogen bonds : angle 4.70530 ( 1179) covalent geometry : bond 0.00475 ( 9336) covalent geometry : angle 0.58094 (12696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7381 (mp0) REVERT: B 128 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8095 (mmt) REVERT: B 137 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6623 (mm-30) REVERT: B 399 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7391 (mp0) outliers start: 17 outliers final: 10 residues processed: 116 average time/residue: 2.0192 time to fit residues: 255.0576 Evaluate side-chains 112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 477 GLN A 555 GLN B 555 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123188 restraints weight = 32659.236| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.11 r_work: 0.3340 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9336 Z= 0.134 Angle : 0.531 4.306 12696 Z= 0.268 Chirality : 0.040 0.140 1368 Planarity : 0.004 0.040 1608 Dihedral : 10.731 168.938 1414 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.08 % Allowed : 18.30 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.26), residues: 1094 helix: 1.81 (0.24), residues: 476 sheet: -0.09 (0.39), residues: 174 loop : 0.14 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.005 0.001 HIS B 181 PHE 0.017 0.001 PHE A 582 TYR 0.011 0.001 TYR B 512 ARG 0.002 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 413) hydrogen bonds : angle 4.51723 ( 1179) covalent geometry : bond 0.00327 ( 9336) covalent geometry : angle 0.53088 (12696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7370 (mp0) REVERT: B 137 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6617 (mm-30) REVERT: B 399 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7380 (mp0) REVERT: B 473 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6732 (tmm160) outliers start: 20 outliers final: 10 residues processed: 122 average time/residue: 2.0117 time to fit residues: 268.1474 Evaluate side-chains 115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 555 GLN B 555 GLN B 634 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125246 restraints weight = 32330.822| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.13 r_work: 0.3370 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.002 0.022 9336 Z= 0.097 Angle : 0.495 4.225 12696 Z= 0.250 Chirality : 0.039 0.138 1368 Planarity : 0.004 0.039 1608 Dihedral : 10.427 170.865 1414 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.66 % Allowed : 18.92 % Favored : 79.42 % 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: 1.48 (0.26), residues: 1094 helix: 2.05 (0.24), residues: 476 sheet: 0.04 (0.40), residues: 174 loop : 0.33 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 95 HIS 0.003 0.001 HIS B 181 PHE 0.015 0.001 PHE A 582 TYR 0.010 0.001 TYR A 512 ARG 0.002 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 413) hydrogen bonds : angle 4.33892 ( 1179) covalent geometry : bond 0.00234 ( 9336) covalent geometry : angle 0.49460 (12696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7361 (mp0) REVERT: A 473 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6776 (tmm160) REVERT: B 137 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6566 (mm-30) REVERT: B 399 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7381 (mp0) REVERT: B 473 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6777 (tmm160) REVERT: B 594 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8275 (mm110) outliers start: 16 outliers final: 5 residues processed: 127 average time/residue: 1.9824 time to fit residues: 275.3977 Evaluate side-chains 117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 555 GLN B 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125522 restraints weight = 32326.213| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.13 r_work: 0.3373 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9336 Z= 0.097 Angle : 0.492 4.530 12696 Z= 0.247 Chirality : 0.039 0.137 1368 Planarity : 0.004 0.038 1608 Dihedral : 10.323 170.847 1414 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.77 % Allowed : 19.33 % Favored : 78.90 % 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: 1.67 (0.26), residues: 1094 helix: 2.21 (0.24), residues: 476 sheet: 0.08 (0.40), residues: 174 loop : 0.45 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 59 HIS 0.003 0.001 HIS B 181 PHE 0.015 0.001 PHE A 582 TYR 0.010 0.001 TYR A 512 ARG 0.004 0.000 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.02880 ( 413) hydrogen bonds : angle 4.23362 ( 1179) covalent geometry : bond 0.00236 ( 9336) covalent geometry : angle 0.49249 (12696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7358 (mp0) REVERT: A 473 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7172 (tmm160) REVERT: B 137 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6568 (mm-30) REVERT: B 399 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7371 (mp0) REVERT: B 473 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7146 (tmm160) outliers start: 17 outliers final: 7 residues processed: 122 average time/residue: 1.9667 time to fit residues: 261.9520 Evaluate side-chains 116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.154919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125730 restraints weight = 32393.603| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.14 r_work: 0.3374 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9336 Z= 0.101 Angle : 0.494 4.518 12696 Z= 0.248 Chirality : 0.039 0.137 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.310 170.799 1414 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.77 % Allowed : 19.85 % Favored : 78.38 % 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: 1.74 (0.26), residues: 1094 helix: 2.27 (0.24), residues: 476 sheet: 0.10 (0.40), residues: 174 loop : 0.49 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 59 HIS 0.003 0.001 HIS A 181 PHE 0.015 0.001 PHE A 582 TYR 0.010 0.001 TYR A 512 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 413) hydrogen bonds : angle 4.20312 ( 1179) covalent geometry : bond 0.00244 ( 9336) covalent geometry : angle 0.49448 (12696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7374 (mp0) REVERT: A 473 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7175 (tmm160) REVERT: B 137 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6557 (mm-30) REVERT: B 399 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7374 (mp0) REVERT: B 473 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7141 (tmm160) REVERT: B 594 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8238 (mm110) outliers start: 17 outliers final: 8 residues processed: 116 average time/residue: 2.0619 time to fit residues: 260.3087 Evaluate side-chains 113 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 555 GLN B 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125258 restraints weight = 32379.484| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.14 r_work: 0.3363 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9336 Z= 0.107 Angle : 0.498 4.440 12696 Z= 0.250 Chirality : 0.039 0.136 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.337 170.108 1414 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.66 % Allowed : 20.06 % Favored : 78.27 % 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: 1.77 (0.27), residues: 1094 helix: 2.31 (0.24), residues: 476 sheet: 0.06 (0.41), residues: 174 loop : 0.51 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 59 HIS 0.005 0.001 HIS A 181 PHE 0.015 0.001 PHE A 582 TYR 0.011 0.001 TYR B 512 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 413) hydrogen bonds : angle 4.17202 ( 1179) covalent geometry : bond 0.00263 ( 9336) covalent geometry : angle 0.49802 (12696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.7669 (m-30) cc_final: 0.7210 (t70) REVERT: A 399 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7402 (mp0) REVERT: A 473 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7186 (tmm160) REVERT: B 137 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6564 (mm-30) REVERT: B 188 ASP cc_start: 0.7604 (m-30) cc_final: 0.7103 (t70) REVERT: B 399 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7424 (mp0) REVERT: B 473 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7160 (tmm160) outliers start: 16 outliers final: 8 residues processed: 115 average time/residue: 2.1501 time to fit residues: 269.7655 Evaluate side-chains 112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 94 optimal weight: 0.1980 chunk 76 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 555 GLN B 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127190 restraints weight = 32141.218| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.13 r_work: 0.3420 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9336 Z= 0.089 Angle : 0.481 4.404 12696 Z= 0.241 Chirality : 0.038 0.136 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.228 172.117 1414 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.35 % Allowed : 20.17 % Favored : 78.48 % 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: 1.99 (0.27), residues: 1094 helix: 2.44 (0.24), residues: 476 sheet: 0.27 (0.41), residues: 170 loop : 0.64 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 59 HIS 0.004 0.001 HIS A 181 PHE 0.014 0.001 PHE A 582 TYR 0.009 0.001 TYR A 512 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.02690 ( 413) hydrogen bonds : angle 4.08112 ( 1179) covalent geometry : bond 0.00216 ( 9336) covalent geometry : angle 0.48060 (12696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.7612 (m-30) cc_final: 0.7166 (t70) REVERT: A 287 ILE cc_start: 0.7446 (mt) cc_final: 0.7213 (mm) REVERT: A 399 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7437 (mp0) REVERT: A 473 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7229 (tmm160) REVERT: B 137 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6566 (mm-30) REVERT: B 188 ASP cc_start: 0.7569 (m-30) cc_final: 0.7057 (t70) REVERT: B 287 ILE cc_start: 0.7459 (mt) cc_final: 0.7224 (mm) REVERT: B 399 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7445 (mp0) REVERT: B 473 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7198 (tmm160) outliers start: 13 outliers final: 5 residues processed: 116 average time/residue: 2.0669 time to fit residues: 261.6808 Evaluate side-chains 109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124669 restraints weight = 32307.025| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.14 r_work: 0.3356 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9336 Z= 0.132 Angle : 0.520 5.554 12696 Z= 0.260 Chirality : 0.041 0.161 1368 Planarity : 0.004 0.037 1608 Dihedral : 10.414 168.302 1414 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.94 % Allowed : 20.69 % Favored : 78.38 % 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: 1.86 (0.27), residues: 1094 helix: 2.37 (0.24), residues: 476 sheet: 0.20 (0.41), residues: 168 loop : 0.53 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 59 HIS 0.003 0.001 HIS A 181 PHE 0.016 0.001 PHE B 582 TYR 0.014 0.001 TYR B 512 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 413) hydrogen bonds : angle 4.17905 ( 1179) covalent geometry : bond 0.00324 ( 9336) covalent geometry : angle 0.51995 (12696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11212.47 seconds wall clock time: 192 minutes 26.60 seconds (11546.60 seconds total)