Starting phenix.real_space_refine on Sat Jun 7 12:06:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpg_16152/06_2025/8bpg_16152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpg_16152/06_2025/8bpg_16152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bpg_16152/06_2025/8bpg_16152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpg_16152/06_2025/8bpg_16152.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpg_16152/06_2025/8bpg_16152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpg_16152/06_2025/8bpg_16152.cif" } resolution = 3.1 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= 0.008 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 46 5.16 5 C 5444 2.51 5 N 1468 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8650 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, H, B, F Time building chain proxies: 6.40, per 1000 atoms: 0.74 Number of scatterers: 8650 At special positions: 0 Unit cell: (117.72, 124.2, 102.6, 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 46 16.00 O 1692 8.00 N 1468 7.00 C 5444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 601 " - " ASN C 563 " " NAG F 601 " - " ASN F 563 " " NAG G 1 " - " ASN D 563 " " NAG H 1 " - " ASN E 563 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 982.6 milliseconds 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: 2096 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 26 sheets defined 11.9% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.815A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 466 removed outlier: 3.765A pdb=" N ASN D 465 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 466 " --> pdb=" O GLN D 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 462 through 466' Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.604A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 525 through 530 Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.815A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.764A pdb=" N ASN E 465 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 466 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 466' Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 420 removed outlier: 3.603A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 Processing helix chain 'F' and resid 525 through 530 Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS B 37 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 86 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR B 81 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AA3, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 380 through 384 removed outlier: 3.528A pdb=" N CYS D 426 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 439 " --> pdb=" O CYS D 426 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 428 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 399 through 400 removed outlier: 3.756A pdb=" N THR D 404 " --> pdb=" O HIS D 400 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AA9, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG C 346 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.866A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 441 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 485 through 489 removed outlier: 3.604A pdb=" N THR C 535 " --> pdb=" O MET C 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS A 37 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A 86 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 81 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AB7, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG E 346 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 380 through 384 removed outlier: 3.528A pdb=" N CYS E 426 " --> pdb=" O GLN E 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 439 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 428 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 399 through 400 removed outlier: 3.756A pdb=" N THR E 404 " --> pdb=" O HIS E 400 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AC4, first strand: chain 'F' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG F 346 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 379 through 383 removed outlier: 3.865A pdb=" N THR F 379 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE F 424 " --> pdb=" O ILE F 441 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 441 " --> pdb=" O PHE F 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 485 through 489 removed outlier: 3.606A pdb=" N THR F 535 " --> pdb=" O MET F 489 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 786 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: 2.38 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2096 1.33 - 1.45: 1768 1.45 - 1.58: 4924 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 8852 Sorted by residual: bond pdb=" N VAL C 547 " pdb=" CA VAL C 547 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.14e-02 7.69e+03 1.34e+01 bond pdb=" N VAL F 547 " pdb=" CA VAL F 547 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" N VAL F 523 " pdb=" CA VAL F 523 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.15e-02 7.56e+03 1.07e+01 bond pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N VAL C 523 " pdb=" CA VAL C 523 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.15e-02 7.56e+03 1.05e+01 ... (remaining 8847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 9252 1.22 - 2.44: 2203 2.44 - 3.66: 565 3.66 - 4.88: 60 4.88 - 6.10: 10 Bond angle restraints: 12090 Sorted by residual: angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" O GLY B 107 " ideal model delta sigma weight residual 122.29 118.24 4.05 8.10e-01 1.52e+00 2.49e+01 angle pdb=" CA GLY A 107 " pdb=" C GLY A 107 " pdb=" O GLY A 107 " ideal model delta sigma weight residual 122.29 118.25 4.04 8.10e-01 1.52e+00 2.49e+01 angle pdb=" N LEU E 466 " pdb=" CA LEU E 466 " pdb=" C LEU E 466 " ideal model delta sigma weight residual 113.18 108.06 5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" N LEU D 466 " pdb=" CA LEU D 466 " pdb=" C LEU D 466 " ideal model delta sigma weight residual 113.18 108.08 5.10 1.21e+00 6.83e-01 1.78e+01 angle pdb=" N ASN F 545 " pdb=" CA ASN F 545 " pdb=" C ASN F 545 " ideal model delta sigma weight residual 112.92 108.09 4.83 1.23e+00 6.61e-01 1.54e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 4910 16.02 - 32.04: 392 32.04 - 48.06: 106 48.06 - 64.08: 26 64.08 - 80.10: 4 Dihedral angle restraints: 5438 sinusoidal: 2210 harmonic: 3228 Sorted by residual: dihedral pdb=" CA CYS F 414 " pdb=" C CYS F 414 " pdb=" N GLU F 415 " pdb=" CA GLU F 415 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA CYS C 414 " pdb=" C CYS C 414 " pdb=" N GLU C 415 " pdb=" CA GLU C 415 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CG ARG A 83 " pdb=" CD ARG A 83 " pdb=" NE ARG A 83 " pdb=" CZ ARG A 83 " ideal model delta sinusoidal sigma weight residual 180.00 136.71 43.29 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 5435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1394 0.165 - 0.331: 44 0.331 - 0.496: 0 0.496 - 0.661: 0 0.661 - 0.827: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 563 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.39e+01 ... (remaining 1437 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 514 " -0.207 9.50e-02 1.11e+02 9.26e-02 5.28e+00 pdb=" NE ARG C 514 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 514 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 514 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 514 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 514 " 0.206 9.50e-02 1.11e+02 9.24e-02 5.24e+00 pdb=" NE ARG F 514 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 514 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 514 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 514 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 50 " 0.187 9.50e-02 1.11e+02 8.39e-02 4.34e+00 pdb=" NE ARG A 50 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 50 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 50 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 50 " 0.006 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 52 2.60 - 3.18: 7094 3.18 - 3.75: 12278 3.75 - 4.33: 16814 4.33 - 4.90: 27963 Nonbonded interactions: 64201 Sorted by model distance: nonbonded pdb=" SG CYS B 49 " pdb=" SG CYS B 58 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS A 49 " pdb=" SG CYS A 58 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 37 " pdb=" SG CYS B 104 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS A 37 " pdb=" SG CYS A 104 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 474 " pdb=" SG CYS D 536 " model vdw 2.037 3.760 ... (remaining 64196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 3.580 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.520 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 0.052 8862 Z= 0.710 Angle : 1.120 7.414 12116 Z= 0.804 Chirality : 0.079 0.827 1440 Planarity : 0.008 0.093 1538 Dihedral : 12.890 80.095 3330 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.90 (0.25), residues: 1094 helix: -1.03 (0.46), residues: 114 sheet: 0.86 (0.25), residues: 436 loop : -1.80 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 528 HIS 0.006 0.001 HIS A 43 PHE 0.016 0.002 PHE D 516 TYR 0.012 0.001 TYR E 500 ARG 0.003 0.000 ARG B 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 4) link_NAG-ASN : angle 4.96375 ( 12) link_BETA1-4 : bond 0.01674 ( 2) link_BETA1-4 : angle 3.38065 ( 6) hydrogen bonds : bond 0.22214 ( 240) hydrogen bonds : angle 8.84609 ( 786) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.10721 ( 8) covalent geometry : bond 0.00964 ( 8852) covalent geometry : angle 1.10803 (12090) *********************** 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 240 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.6979 (p) cc_final: 0.6749 (p) REVERT: C 463 GLN cc_start: 0.6731 (tt0) cc_final: 0.6483 (tt0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3082 time to fit residues: 92.3745 Evaluate side-chains 144 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN D 510 GLN C 439 GLN C 490 GLN A 43 HIS ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN E 510 GLN F 490 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.089855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062896 restraints weight = 27308.746| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.38 r_work: 0.3121 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8862 Z= 0.155 Angle : 0.669 7.024 12116 Z= 0.346 Chirality : 0.046 0.220 1440 Planarity : 0.004 0.024 1538 Dihedral : 4.679 33.081 1312 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.14 % Allowed : 10.31 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.46 (0.25), residues: 1094 helix: -1.24 (0.43), residues: 112 sheet: 1.33 (0.25), residues: 426 loop : -1.50 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.009 0.002 HIS D 400 PHE 0.014 0.002 PHE D 479 TYR 0.019 0.001 TYR E 375 ARG 0.005 0.001 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 4) link_NAG-ASN : angle 1.67634 ( 12) link_BETA1-4 : bond 0.00536 ( 2) link_BETA1-4 : angle 1.05207 ( 6) hydrogen bonds : bond 0.04595 ( 240) hydrogen bonds : angle 6.48897 ( 786) SS BOND : bond 0.00507 ( 4) SS BOND : angle 0.47564 ( 8) covalent geometry : bond 0.00360 ( 8852) covalent geometry : angle 0.66668 (12090) *********************** 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 183 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 PHE cc_start: 0.6897 (t80) cc_final: 0.6453 (t80) REVERT: A 93 GLN cc_start: 0.7768 (mp10) cc_final: 0.7324 (mp10) REVERT: E 417 ASP cc_start: 0.8645 (m-30) cc_final: 0.7960 (p0) REVERT: E 489 MET cc_start: 0.8936 (mtp) cc_final: 0.8304 (mmt) REVERT: E 493 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7963 (mm110) REVERT: F 405 PHE cc_start: 0.6887 (t80) cc_final: 0.6307 (t80) REVERT: F 463 GLN cc_start: 0.8489 (tp-100) cc_final: 0.8235 (tp40) REVERT: F 489 MET cc_start: 0.8258 (ttm) cc_final: 0.7871 (mmt) REVERT: F 493 GLN cc_start: 0.8712 (mp10) cc_final: 0.8431 (mp10) outliers start: 21 outliers final: 15 residues processed: 174 average time/residue: 0.2585 time to fit residues: 58.4022 Evaluate side-chains 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 523 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.0770 chunk 37 optimal weight: 0.0770 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.087147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059885 restraints weight = 27680.729| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.49 r_work: 0.3047 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8862 Z= 0.161 Angle : 0.638 7.171 12116 Z= 0.329 Chirality : 0.046 0.193 1440 Planarity : 0.004 0.052 1538 Dihedral : 4.424 25.487 1312 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.78 % Allowed : 13.57 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.58 (0.25), residues: 1094 helix: -1.26 (0.43), residues: 112 sheet: 1.22 (0.24), residues: 424 loop : -1.56 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 488 HIS 0.010 0.002 HIS D 430 PHE 0.017 0.002 PHE D 479 TYR 0.021 0.001 TYR D 375 ARG 0.006 0.001 ARG D 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 1.41308 ( 12) link_BETA1-4 : bond 0.00221 ( 2) link_BETA1-4 : angle 1.29015 ( 6) hydrogen bonds : bond 0.04170 ( 240) hydrogen bonds : angle 5.89602 ( 786) SS BOND : bond 0.00447 ( 4) SS BOND : angle 0.50313 ( 8) covalent geometry : bond 0.00380 ( 8852) covalent geometry : angle 0.63632 (12090) *********************** 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 175 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8937 (mmp80) cc_final: 0.8582 (mmp80) REVERT: C 499 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8033 (ttmm) REVERT: A 93 GLN cc_start: 0.8103 (mp10) cc_final: 0.7723 (mp10) REVERT: E 417 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8085 (p0) REVERT: E 489 MET cc_start: 0.8899 (mtp) cc_final: 0.8285 (mmt) REVERT: E 493 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7839 (mm110) REVERT: E 568 MET cc_start: 0.8435 (mmm) cc_final: 0.8081 (mmm) REVERT: F 405 PHE cc_start: 0.7161 (t80) cc_final: 0.6621 (t80) REVERT: F 423 ARG cc_start: 0.7600 (tmm-80) cc_final: 0.7383 (tmm-80) REVERT: F 489 MET cc_start: 0.8386 (ttm) cc_final: 0.8067 (tpp) REVERT: F 499 LYS cc_start: 0.8259 (mttp) cc_final: 0.8034 (mttp) outliers start: 37 outliers final: 23 residues processed: 158 average time/residue: 0.2615 time to fit residues: 54.0725 Evaluate side-chains 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 523 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0010 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.087092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.059835 restraints weight = 27520.818| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 4.48 r_work: 0.3053 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8862 Z= 0.134 Angle : 0.615 10.326 12116 Z= 0.315 Chirality : 0.045 0.184 1440 Planarity : 0.004 0.070 1538 Dihedral : 4.173 20.472 1312 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.88 % Allowed : 15.10 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.51 (0.25), residues: 1094 helix: -1.15 (0.43), residues: 112 sheet: 1.23 (0.24), residues: 422 loop : -1.48 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 528 HIS 0.005 0.001 HIS E 430 PHE 0.012 0.001 PHE D 479 TYR 0.025 0.001 TYR E 375 ARG 0.006 0.000 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 4) link_NAG-ASN : angle 1.24347 ( 12) link_BETA1-4 : bond 0.00233 ( 2) link_BETA1-4 : angle 1.13818 ( 6) hydrogen bonds : bond 0.03657 ( 240) hydrogen bonds : angle 5.54086 ( 786) SS BOND : bond 0.00414 ( 4) SS BOND : angle 0.34523 ( 8) covalent geometry : bond 0.00314 ( 8852) covalent geometry : angle 0.61377 (12090) *********************** 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 173 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8254 (mm-30) REVERT: B 79 LYS cc_start: 0.8047 (pptt) cc_final: 0.7838 (pptt) REVERT: B 83 ARG cc_start: 0.8941 (mmp80) cc_final: 0.8682 (mmp80) REVERT: B 94 LEU cc_start: 0.8969 (tp) cc_final: 0.8752 (tt) REVERT: C 405 PHE cc_start: 0.7256 (t80) cc_final: 0.6379 (t80) REVERT: C 527 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8776 (mp0) REVERT: A 22 GLU cc_start: 0.8825 (tt0) cc_final: 0.8552 (tp30) REVERT: A 93 GLN cc_start: 0.8194 (mp10) cc_final: 0.7723 (mp10) REVERT: E 417 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8097 (p0) REVERT: E 489 MET cc_start: 0.8919 (mtp) cc_final: 0.7998 (mmm) REVERT: E 493 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7857 (mm110) REVERT: F 423 ARG cc_start: 0.7640 (tmm-80) cc_final: 0.7427 (tmm-80) REVERT: F 489 MET cc_start: 0.8322 (ttm) cc_final: 0.7913 (tpp) REVERT: F 499 LYS cc_start: 0.8286 (mttp) cc_final: 0.7959 (mttp) REVERT: F 527 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8568 (mp0) outliers start: 38 outliers final: 22 residues processed: 161 average time/residue: 0.2560 time to fit residues: 53.5856 Evaluate side-chains 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.085843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058859 restraints weight = 27461.814| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.40 r_work: 0.3026 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8862 Z= 0.152 Angle : 0.626 9.272 12116 Z= 0.319 Chirality : 0.045 0.175 1440 Planarity : 0.004 0.053 1538 Dihedral : 4.077 15.972 1312 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.78 % Allowed : 16.53 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.49 (0.25), residues: 1094 helix: -0.88 (0.46), residues: 100 sheet: 1.16 (0.24), residues: 422 loop : -1.45 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 528 HIS 0.005 0.001 HIS E 393 PHE 0.022 0.002 PHE F 405 TYR 0.015 0.001 TYR C 515 ARG 0.007 0.000 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 4) link_NAG-ASN : angle 1.23461 ( 12) link_BETA1-4 : bond 0.00178 ( 2) link_BETA1-4 : angle 1.22823 ( 6) hydrogen bonds : bond 0.03652 ( 240) hydrogen bonds : angle 5.37805 ( 786) SS BOND : bond 0.00413 ( 4) SS BOND : angle 0.40568 ( 8) covalent geometry : bond 0.00358 ( 8852) covalent geometry : angle 0.62445 (12090) *********************** 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 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8952 (mmp80) cc_final: 0.8720 (mmp80) REVERT: B 94 LEU cc_start: 0.8978 (tp) cc_final: 0.8766 (tt) REVERT: C 405 PHE cc_start: 0.7173 (t80) cc_final: 0.6355 (t80) REVERT: C 493 GLN cc_start: 0.8028 (mp10) cc_final: 0.7739 (mp10) REVERT: C 499 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8277 (ttmm) REVERT: C 527 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8692 (mp0) REVERT: A 24 LYS cc_start: 0.8747 (tptp) cc_final: 0.8229 (tptp) REVERT: A 83 ARG cc_start: 0.9111 (mmp80) cc_final: 0.8864 (mmp80) REVERT: A 93 GLN cc_start: 0.8297 (mp10) cc_final: 0.7761 (mp10) REVERT: E 417 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8216 (p0) REVERT: E 489 MET cc_start: 0.8918 (mtp) cc_final: 0.7963 (mmm) REVERT: F 405 PHE cc_start: 0.7251 (t80) cc_final: 0.6379 (t80) REVERT: F 489 MET cc_start: 0.8261 (ttm) cc_final: 0.7744 (mmt) REVERT: F 499 LYS cc_start: 0.8358 (mttp) cc_final: 0.7991 (mttp) REVERT: F 527 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8544 (mp0) outliers start: 37 outliers final: 26 residues processed: 153 average time/residue: 0.2563 time to fit residues: 51.3652 Evaluate side-chains 149 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.084819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.057817 restraints weight = 27481.774| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 4.39 r_work: 0.2998 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8862 Z= 0.168 Angle : 0.637 10.352 12116 Z= 0.325 Chirality : 0.046 0.171 1440 Planarity : 0.004 0.040 1538 Dihedral : 4.042 14.737 1312 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.08 % Allowed : 17.45 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.61 (0.25), residues: 1094 helix: -0.78 (0.47), residues: 100 sheet: 0.87 (0.23), residues: 446 loop : -1.48 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.005 0.001 HIS E 393 PHE 0.024 0.002 PHE D 405 TYR 0.014 0.001 TYR E 500 ARG 0.006 0.001 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 4) link_NAG-ASN : angle 1.26182 ( 12) link_BETA1-4 : bond 0.00210 ( 2) link_BETA1-4 : angle 1.26713 ( 6) hydrogen bonds : bond 0.03673 ( 240) hydrogen bonds : angle 5.32648 ( 786) SS BOND : bond 0.00468 ( 4) SS BOND : angle 0.41276 ( 8) covalent geometry : bond 0.00397 ( 8852) covalent geometry : angle 0.63523 (12090) *********************** 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 162 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8134 (tptp) REVERT: B 42 MET cc_start: 0.3827 (tmm) cc_final: 0.2964 (tmm) REVERT: B 51 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 83 ARG cc_start: 0.8955 (mmp80) cc_final: 0.8721 (mmp80) REVERT: B 94 LEU cc_start: 0.8963 (tp) cc_final: 0.8725 (tt) REVERT: C 489 MET cc_start: 0.8058 (tpp) cc_final: 0.7835 (tpp) REVERT: C 499 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8294 (ttmm) REVERT: A 24 LYS cc_start: 0.8979 (tptp) cc_final: 0.8428 (tptp) REVERT: A 42 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.4399 (tpp) REVERT: A 81 TYR cc_start: 0.8570 (p90) cc_final: 0.8260 (p90) REVERT: A 93 GLN cc_start: 0.8418 (mp10) cc_final: 0.7908 (mp10) REVERT: E 451 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8843 (ppt90) REVERT: E 489 MET cc_start: 0.8937 (mtp) cc_final: 0.7984 (mmm) REVERT: F 489 MET cc_start: 0.8252 (ttm) cc_final: 0.7715 (mmt) REVERT: F 493 GLN cc_start: 0.8699 (mp10) cc_final: 0.8159 (mp10) REVERT: F 527 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8532 (mp0) REVERT: F 566 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8112 (pp) outliers start: 40 outliers final: 26 residues processed: 150 average time/residue: 0.2548 time to fit residues: 50.3353 Evaluate side-chains 150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.085024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057785 restraints weight = 27946.082| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.44 r_work: 0.3007 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8862 Z= 0.152 Angle : 0.645 9.095 12116 Z= 0.330 Chirality : 0.046 0.174 1440 Planarity : 0.004 0.044 1538 Dihedral : 3.998 18.212 1312 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.78 % Allowed : 19.08 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.58 (0.25), residues: 1094 helix: -0.71 (0.48), residues: 100 sheet: 0.88 (0.23), residues: 446 loop : -1.46 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 528 HIS 0.005 0.001 HIS E 393 PHE 0.025 0.002 PHE C 405 TYR 0.018 0.001 TYR B 72 ARG 0.009 0.000 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 4) link_NAG-ASN : angle 1.20775 ( 12) link_BETA1-4 : bond 0.00301 ( 2) link_BETA1-4 : angle 1.18924 ( 6) hydrogen bonds : bond 0.03570 ( 240) hydrogen bonds : angle 5.15241 ( 786) SS BOND : bond 0.00454 ( 4) SS BOND : angle 0.57531 ( 8) covalent geometry : bond 0.00364 ( 8852) covalent geometry : angle 0.64413 (12090) *********************** 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 160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8953 (tptp) cc_final: 0.8435 (tptp) REVERT: B 51 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8271 (mm-30) REVERT: B 83 ARG cc_start: 0.8939 (mmp80) cc_final: 0.8690 (mmp80) REVERT: B 94 LEU cc_start: 0.8980 (tp) cc_final: 0.8753 (tt) REVERT: C 499 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8377 (ttmm) REVERT: C 527 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8780 (mp0) REVERT: A 24 LYS cc_start: 0.8952 (tptp) cc_final: 0.8399 (tptp) REVERT: A 42 MET cc_start: 0.5936 (mmp) cc_final: 0.4091 (tpp) REVERT: A 68 ILE cc_start: 0.9279 (mp) cc_final: 0.8904 (mt) REVERT: A 83 ARG cc_start: 0.9102 (mmp80) cc_final: 0.8846 (mmp80) REVERT: A 93 GLN cc_start: 0.8424 (mp10) cc_final: 0.7901 (mp10) REVERT: E 451 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8818 (ppt90) REVERT: E 489 MET cc_start: 0.8897 (mtp) cc_final: 0.7968 (mmm) REVERT: F 405 PHE cc_start: 0.7367 (t80) cc_final: 0.6449 (t80) REVERT: F 489 MET cc_start: 0.8234 (ttm) cc_final: 0.7724 (mmt) REVERT: F 493 GLN cc_start: 0.8556 (mp10) cc_final: 0.8050 (mp10) REVERT: F 499 LYS cc_start: 0.8393 (mttp) cc_final: 0.8022 (mttp) REVERT: F 527 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: F 566 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8168 (pp) outliers start: 37 outliers final: 27 residues processed: 151 average time/residue: 0.3007 time to fit residues: 59.7648 Evaluate side-chains 149 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 0.0170 chunk 104 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.083393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056345 restraints weight = 28454.316| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.31 r_work: 0.2972 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8862 Z= 0.205 Angle : 0.667 8.989 12116 Z= 0.344 Chirality : 0.046 0.175 1440 Planarity : 0.004 0.036 1538 Dihedral : 4.181 18.059 1312 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.39 % Allowed : 19.29 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.25), residues: 1094 helix: -0.75 (0.48), residues: 100 sheet: 0.75 (0.23), residues: 446 loop : -1.47 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.007 0.001 HIS E 393 PHE 0.019 0.002 PHE D 405 TYR 0.017 0.002 TYR E 500 ARG 0.009 0.001 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 4) link_NAG-ASN : angle 1.42582 ( 12) link_BETA1-4 : bond 0.00207 ( 2) link_BETA1-4 : angle 1.39418 ( 6) hydrogen bonds : bond 0.04012 ( 240) hydrogen bonds : angle 5.35536 ( 786) SS BOND : bond 0.00569 ( 4) SS BOND : angle 0.74083 ( 8) covalent geometry : bond 0.00488 ( 8852) covalent geometry : angle 0.66526 (12090) *********************** 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 162 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8954 (tptp) cc_final: 0.8379 (tptp) REVERT: B 83 ARG cc_start: 0.8965 (mmp80) cc_final: 0.8657 (mmp80) REVERT: B 94 LEU cc_start: 0.8955 (tp) cc_final: 0.8722 (tt) REVERT: D 445 LYS cc_start: 0.8761 (tppt) cc_final: 0.8467 (tppt) REVERT: C 405 PHE cc_start: 0.7247 (t80) cc_final: 0.6379 (t80) REVERT: C 499 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8429 (ttmm) REVERT: A 24 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8541 (tptp) REVERT: A 42 MET cc_start: 0.5889 (mmp) cc_final: 0.4115 (tpp) REVERT: A 93 GLN cc_start: 0.8530 (mp10) cc_final: 0.8095 (mp10) REVERT: E 451 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8729 (ppt90) REVERT: F 489 MET cc_start: 0.8264 (ttm) cc_final: 0.7513 (mmm) REVERT: F 493 GLN cc_start: 0.8554 (mp10) cc_final: 0.7747 (mp10) REVERT: F 499 LYS cc_start: 0.8418 (mttp) cc_final: 0.8044 (mttp) REVERT: F 527 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: F 566 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8173 (pp) outliers start: 43 outliers final: 32 residues processed: 151 average time/residue: 0.2870 time to fit residues: 56.2734 Evaluate side-chains 149 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 32 optimal weight: 0.0020 chunk 90 optimal weight: 0.0970 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 58 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS D 510 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.086070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059275 restraints weight = 27613.284| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.39 r_work: 0.3048 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8862 Z= 0.115 Angle : 0.650 9.682 12116 Z= 0.329 Chirality : 0.045 0.185 1440 Planarity : 0.004 0.043 1538 Dihedral : 3.918 25.255 1312 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.27 % Allowed : 20.51 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.53 (0.25), residues: 1094 helix: -0.69 (0.48), residues: 100 sheet: 0.90 (0.23), residues: 452 loop : -1.43 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 528 HIS 0.006 0.001 HIS D 400 PHE 0.030 0.001 PHE F 405 TYR 0.012 0.001 TYR C 515 ARG 0.010 0.001 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 1.11081 ( 12) link_BETA1-4 : bond 0.00372 ( 2) link_BETA1-4 : angle 0.96148 ( 6) hydrogen bonds : bond 0.03198 ( 240) hydrogen bonds : angle 4.86362 ( 786) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.49957 ( 8) covalent geometry : bond 0.00264 ( 8852) covalent geometry : angle 0.64908 (12090) *********************** 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 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8936 (tptp) cc_final: 0.8318 (tptp) REVERT: B 83 ARG cc_start: 0.8928 (mmp80) cc_final: 0.8647 (mmp80) REVERT: B 94 LEU cc_start: 0.8945 (tp) cc_final: 0.8682 (tt) REVERT: D 445 LYS cc_start: 0.8734 (tppt) cc_final: 0.8406 (tppt) REVERT: C 405 PHE cc_start: 0.7279 (t80) cc_final: 0.6386 (t80) REVERT: C 499 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8431 (ttmm) REVERT: C 527 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: A 24 LYS cc_start: 0.9077 (tptp) cc_final: 0.8614 (tptp) REVERT: A 29 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 42 MET cc_start: 0.5802 (mmp) cc_final: 0.4743 (tpp) REVERT: A 93 GLN cc_start: 0.8531 (mp10) cc_final: 0.8090 (mp10) REVERT: E 417 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8251 (p0) REVERT: E 451 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8756 (ppt90) REVERT: E 489 MET cc_start: 0.8928 (mtp) cc_final: 0.8375 (mmp) REVERT: E 493 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7797 (tp40) REVERT: F 405 PHE cc_start: 0.7404 (t80) cc_final: 0.6543 (t80) REVERT: F 489 MET cc_start: 0.8142 (ttm) cc_final: 0.7562 (mmt) REVERT: F 493 GLN cc_start: 0.8409 (mp10) cc_final: 0.8097 (mp10) REVERT: F 527 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: F 566 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8057 (pp) outliers start: 32 outliers final: 20 residues processed: 155 average time/residue: 0.2723 time to fit residues: 54.5201 Evaluate side-chains 147 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS D 510 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.084724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058097 restraints weight = 28258.889| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.23 r_work: 0.3019 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8862 Z= 0.142 Angle : 0.663 9.211 12116 Z= 0.337 Chirality : 0.045 0.206 1440 Planarity : 0.004 0.042 1538 Dihedral : 3.937 29.544 1312 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.47 % Allowed : 21.02 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.74 (0.47), residues: 100 sheet: 0.96 (0.24), residues: 440 loop : -1.44 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.008 0.001 HIS D 400 PHE 0.026 0.002 PHE F 405 TYR 0.016 0.001 TYR C 515 ARG 0.014 0.001 ARG A 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 4) link_NAG-ASN : angle 1.18567 ( 12) link_BETA1-4 : bond 0.00341 ( 2) link_BETA1-4 : angle 1.13598 ( 6) hydrogen bonds : bond 0.03466 ( 240) hydrogen bonds : angle 4.98402 ( 786) SS BOND : bond 0.00375 ( 4) SS BOND : angle 0.46644 ( 8) covalent geometry : bond 0.00345 ( 8852) covalent geometry : angle 0.66210 (12090) ********************** 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 154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8911 (tptp) cc_final: 0.8284 (tptp) REVERT: B 42 MET cc_start: 0.5180 (tpt) cc_final: 0.4523 (tmm) REVERT: B 83 ARG cc_start: 0.8931 (mmp80) cc_final: 0.8606 (mmp80) REVERT: B 94 LEU cc_start: 0.8986 (tp) cc_final: 0.8777 (tt) REVERT: D 417 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8499 (p0) REVERT: D 445 LYS cc_start: 0.8753 (tppt) cc_final: 0.8431 (tppt) REVERT: C 405 PHE cc_start: 0.7377 (t80) cc_final: 0.6483 (t80) REVERT: C 499 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8406 (ttmm) REVERT: C 527 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8815 (mp0) REVERT: A 24 LYS cc_start: 0.9090 (tptp) cc_final: 0.8635 (tptp) REVERT: A 42 MET cc_start: 0.5740 (mmp) cc_final: 0.3937 (tpp) REVERT: A 93 GLN cc_start: 0.8550 (mp10) cc_final: 0.8112 (mp10) REVERT: E 417 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8298 (p0) REVERT: E 451 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8695 (ppt90) REVERT: E 489 MET cc_start: 0.8945 (mtp) cc_final: 0.8180 (mmm) REVERT: E 493 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7804 (tp40) REVERT: F 489 MET cc_start: 0.8177 (ttm) cc_final: 0.7631 (mmt) REVERT: F 493 GLN cc_start: 0.8408 (mp10) cc_final: 0.7892 (mp10) REVERT: F 499 LYS cc_start: 0.8401 (mttp) cc_final: 0.8026 (mttp) REVERT: F 527 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: F 566 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8131 (pp) outliers start: 34 outliers final: 27 residues processed: 144 average time/residue: 0.2606 time to fit residues: 48.8267 Evaluate side-chains 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.0870 chunk 86 optimal weight: 0.0370 chunk 82 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 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 = 0.3827 r_free = 0.3827 target = 0.085382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.058754 restraints weight = 27670.312| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.33 r_work: 0.3036 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8862 Z= 0.119 Angle : 0.651 9.457 12116 Z= 0.330 Chirality : 0.045 0.182 1440 Planarity : 0.004 0.052 1538 Dihedral : 3.930 28.668 1312 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.67 % Allowed : 20.61 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.52 (0.25), residues: 1094 helix: -0.69 (0.47), residues: 100 sheet: 0.92 (0.24), residues: 448 loop : -1.41 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.006 0.001 HIS D 400 PHE 0.018 0.001 PHE D 405 TYR 0.013 0.001 TYR C 515 ARG 0.012 0.001 ARG A 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 1.03923 ( 12) link_BETA1-4 : bond 0.00251 ( 2) link_BETA1-4 : angle 1.00078 ( 6) hydrogen bonds : bond 0.03228 ( 240) hydrogen bonds : angle 4.86359 ( 786) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.48454 ( 8) covalent geometry : bond 0.00285 ( 8852) covalent geometry : angle 0.65039 (12090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5904.32 seconds wall clock time: 103 minutes 24.41 seconds (6204.41 seconds total)