Starting phenix.real_space_refine on Sat Oct 11 01:54:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymm_39399/10_2025/8ymm_39399_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymm_39399/10_2025/8ymm_39399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ymm_39399/10_2025/8ymm_39399_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymm_39399/10_2025/8ymm_39399_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ymm_39399/10_2025/8ymm_39399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymm_39399/10_2025/8ymm_39399.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 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 52 5.16 5 C 7070 2.51 5 N 1758 2.21 5 O 1830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10710 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5346 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 35, 'TRANS': 628} Chain breaks: 2 Chain: "B" Number of atoms: 5346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5346 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 35, 'TRANS': 628} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.98, per 1000 atoms: 0.18 Number of scatterers: 10710 At special positions: 0 Unit cell: (148.75, 81.55, 85.05, 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 52 16.00 O 1830 8.00 N 1758 7.00 C 7070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 380.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 2 sheets defined 73.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 3.649A pdb=" N GLN A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 removed outlier: 4.007A pdb=" N ARG A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.660A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.516A pdb=" N PHE A 72 " --> pdb=" O TYR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 92 through 117 removed outlier: 3.966A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 160 through 194 Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.115A pdb=" N PHE A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.863A pdb=" N LEU A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 removed outlier: 4.535A pdb=" N TYR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 296 through 315 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.752A pdb=" N ALA A 366 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 389 Processing helix chain 'A' and resid 390 through 407 Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.627A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 457 through 477 Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.582A pdb=" N LYS A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 535 through 547 Processing helix chain 'A' and resid 566 through 588 Proline residue: A 572 - end of helix Proline residue: A 586 - end of helix Processing helix chain 'A' and resid 590 through 613 removed outlier: 4.316A pdb=" N PHE A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 650 Processing helix chain 'A' and resid 655 through 660 Processing helix chain 'A' and resid 660 through 677 removed outlier: 4.196A pdb=" N VAL A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.696A pdb=" N VAL A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 704 through 711 removed outlier: 3.873A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'B' and resid 3 through 31 removed outlier: 3.649A pdb=" N GLN B 31 " --> pdb=" O PHE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 removed outlier: 4.007A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 45 removed outlier: 3.660A pdb=" N TYR B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.516A pdb=" N PHE B 72 " --> pdb=" O TYR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 92 through 117 removed outlier: 3.966A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 160 through 194 Processing helix chain 'B' and resid 198 through 202 removed outlier: 4.115A pdb=" N PHE B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 242 through 259 removed outlier: 3.863A pdb=" N LEU B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 267 removed outlier: 4.535A pdb=" N TYR B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 296 through 315 Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.752A pdb=" N ALA B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 389 Processing helix chain 'B' and resid 390 through 407 Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.627A pdb=" N PHE B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 457 through 477 Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.584A pdb=" N LYS B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 525 Processing helix chain 'B' and resid 526 through 535 Processing helix chain 'B' and resid 535 through 547 Processing helix chain 'B' and resid 566 through 588 Proline residue: B 572 - end of helix Proline residue: B 586 - end of helix Processing helix chain 'B' and resid 590 through 613 removed outlier: 4.316A pdb=" N PHE B 594 " --> pdb=" O MET B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 650 Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 660 through 677 removed outlier: 4.196A pdb=" N VAL B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.696A pdb=" N VAL B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 700 Processing helix chain 'B' and resid 704 through 711 removed outlier: 3.873A pdb=" N TYR B 708 " --> pdb=" O ASN B 704 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing sheet with id=AA1, first strand: chain 'A' and resid 238 through 240 removed outlier: 4.796A pdb=" N VAL A 239 " --> pdb=" O MET A 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 240 removed outlier: 4.796A pdb=" N VAL B 239 " --> pdb=" O MET B 321 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1962 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: 1.45 Time building geometry restraints manager: 1.13 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: 2469 1.33 - 1.45: 2331 1.45 - 1.57: 6110 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11002 Sorted by residual: bond pdb=" CA ILE B 392 " pdb=" CB ILE B 392 " ideal model delta sigma weight residual 1.539 1.563 -0.024 5.40e-03 3.43e+04 2.04e+01 bond pdb=" CA ILE A 392 " pdb=" CB ILE A 392 " ideal model delta sigma weight residual 1.539 1.563 -0.024 5.40e-03 3.43e+04 2.04e+01 bond pdb=" C TYR A 684 " pdb=" N PRO A 685 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.20e-02 6.94e+03 1.53e+01 bond pdb=" C TYR B 684 " pdb=" N PRO B 685 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.20e-02 6.94e+03 1.53e+01 bond pdb=" CA ILE B 510 " pdb=" CB ILE B 510 " ideal model delta sigma weight residual 1.537 1.555 -0.018 5.00e-03 4.00e+04 1.33e+01 ... (remaining 10997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 14251 2.77 - 5.53: 547 5.53 - 8.30: 126 8.30 - 11.07: 22 11.07 - 13.84: 6 Bond angle restraints: 14952 Sorted by residual: angle pdb=" N TYR A 69 " pdb=" CA TYR A 69 " pdb=" C TYR A 69 " ideal model delta sigma weight residual 113.88 105.92 7.96 1.23e+00 6.61e-01 4.18e+01 angle pdb=" N TYR B 69 " pdb=" CA TYR B 69 " pdb=" C TYR B 69 " ideal model delta sigma weight residual 113.88 105.92 7.96 1.23e+00 6.61e-01 4.18e+01 angle pdb=" N LYS B 318 " pdb=" CA LYS B 318 " pdb=" C LYS B 318 " ideal model delta sigma weight residual 114.12 105.61 8.51 1.39e+00 5.18e-01 3.75e+01 angle pdb=" N LYS A 318 " pdb=" CA LYS A 318 " pdb=" C LYS A 318 " ideal model delta sigma weight residual 114.12 105.61 8.51 1.39e+00 5.18e-01 3.75e+01 angle pdb=" N ILE B 296 " pdb=" CA ILE B 296 " pdb=" C ILE B 296 " ideal model delta sigma weight residual 109.34 121.57 -12.23 2.08e+00 2.31e-01 3.46e+01 ... (remaining 14947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 5303 22.20 - 44.40: 729 44.40 - 66.60: 426 66.60 - 88.80: 26 88.80 - 111.00: 2 Dihedral angle restraints: 6486 sinusoidal: 2584 harmonic: 3902 Sorted by residual: dihedral pdb=" C HIS B 715 " pdb=" N HIS B 715 " pdb=" CA HIS B 715 " pdb=" CB HIS B 715 " ideal model delta harmonic sigma weight residual -122.60 -138.15 15.55 0 2.50e+00 1.60e-01 3.87e+01 dihedral pdb=" C HIS A 715 " pdb=" N HIS A 715 " pdb=" CA HIS A 715 " pdb=" CB HIS A 715 " ideal model delta harmonic sigma weight residual -122.60 -138.15 15.55 0 2.50e+00 1.60e-01 3.87e+01 dihedral pdb=" C ILE B 510 " pdb=" N ILE B 510 " pdb=" CA ILE B 510 " pdb=" CB ILE B 510 " ideal model delta harmonic sigma weight residual -122.00 -137.25 15.25 0 2.50e+00 1.60e-01 3.72e+01 ... (remaining 6483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1347 0.106 - 0.213: 229 0.213 - 0.319: 72 0.319 - 0.426: 20 0.426 - 0.532: 10 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA TRP B 625 " pdb=" N TRP B 625 " pdb=" C TRP B 625 " pdb=" CB TRP B 625 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA TRP A 625 " pdb=" N TRP A 625 " pdb=" C TRP A 625 " pdb=" CB TRP A 625 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA ILE A 510 " pdb=" N ILE A 510 " pdb=" C ILE A 510 " pdb=" CB ILE A 510 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.53 2.00e-01 2.50e+01 6.94e+00 ... (remaining 1675 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 625 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 626 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 625 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 626 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 626 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 626 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 502 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO B 503 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 503 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 503 " -0.032 5.00e-02 4.00e+02 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 9 2.39 - 3.02: 6250 3.02 - 3.65: 17385 3.65 - 4.27: 29674 4.27 - 4.90: 44709 Nonbonded interactions: 98027 Sorted by model distance: nonbonded pdb=" NH1 ARG A 676 " pdb=" OD1 ASN B 345 " model vdw 1.766 3.120 nonbonded pdb=" OD1 ASN A 345 " pdb=" NH1 ARG B 676 " model vdw 1.766 3.120 nonbonded pdb=" OD1 ASN A 345 " pdb=" CZ ARG B 676 " model vdw 2.066 3.270 nonbonded pdb=" CZ ARG A 676 " pdb=" OD1 ASN B 345 " model vdw 2.066 3.270 nonbonded pdb=" O GLN A 339 " pdb=" O GLN B 339 " model vdw 2.182 3.040 ... (remaining 98022 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 33.660 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: 0.730 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 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 : 0.008 0.047 11002 Z= 0.592 Angle : 1.352 13.835 14952 Z= 0.864 Chirality : 0.104 0.532 1678 Planarity : 0.008 0.066 1872 Dihedral : 24.374 111.002 3962 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 1.67 % Allowed : 9.73 % Favored : 88.60 % Rotamer: Outliers : 34.68 % Allowed : 15.14 % Favored : 50.18 % Cbeta Deviations : 1.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.20), residues: 1316 helix: -1.33 (0.15), residues: 858 sheet: -3.58 (0.77), residues: 36 loop : -3.44 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 67 TYR 0.012 0.002 TYR A 295 PHE 0.021 0.003 PHE A 72 TRP 0.017 0.002 TRP B 625 HIS 0.004 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00801 (11002) covalent geometry : angle 1.35230 (14952) hydrogen bonds : bond 0.17897 ( 662) hydrogen bonds : angle 7.69104 ( 1962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 394 poor density : 242 time to evaluate : 0.380 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7585 (tttt) REVERT: A 85 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.5293 (tmt170) REVERT: A 159 PHE cc_start: 0.3749 (OUTLIER) cc_final: 0.3443 (t80) REVERT: A 228 ASN cc_start: 0.7032 (m110) cc_final: 0.6617 (m-40) REVERT: A 258 TRP cc_start: 0.3263 (OUTLIER) cc_final: 0.2051 (t60) REVERT: A 294 HIS cc_start: 0.1831 (OUTLIER) cc_final: 0.1038 (t-90) REVERT: B 41 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7574 (tttt) REVERT: B 85 ARG cc_start: 0.5710 (OUTLIER) cc_final: 0.5268 (tmt170) REVERT: B 228 ASN cc_start: 0.7012 (m110) cc_final: 0.6641 (m-40) REVERT: B 258 TRP cc_start: 0.3261 (OUTLIER) cc_final: 0.2077 (t60) REVERT: B 294 HIS cc_start: 0.1801 (OUTLIER) cc_final: 0.1024 (t-90) outliers start: 394 outliers final: 38 residues processed: 530 average time/residue: 0.4577 time to fit residues: 262.8545 Evaluate side-chains 179 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 90 HIS A 124 ASN A 208 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN A 501 GLN ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 575 GLN A 609 GLN A 615 ASN A 616 GLN B 74 HIS B 90 HIS B 124 ASN B 208 ASN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN B 501 GLN ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 575 GLN B 609 GLN B 615 ASN B 616 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122119 restraints weight = 11523.989| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.02 r_work: 0.3093 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11002 Z= 0.186 Angle : 0.771 11.895 14952 Z= 0.392 Chirality : 0.049 0.277 1678 Planarity : 0.007 0.059 1872 Dihedral : 10.922 80.485 1568 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.90 % Favored : 91.79 % Rotamer: Outliers : 9.07 % Allowed : 25.79 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.23), residues: 1316 helix: 0.39 (0.17), residues: 854 sheet: -3.18 (0.72), residues: 36 loop : -3.01 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 45 TYR 0.019 0.002 TYR A 295 PHE 0.023 0.002 PHE B 390 TRP 0.032 0.002 TRP A 625 HIS 0.004 0.001 HIS A 651 Details of bonding type rmsd covalent geometry : bond 0.00428 (11002) covalent geometry : angle 0.77059 (14952) hydrogen bonds : bond 0.04992 ( 662) hydrogen bonds : angle 5.52187 ( 1962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 144 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 85 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6904 (tpt170) REVERT: A 159 PHE cc_start: 0.6242 (OUTLIER) cc_final: 0.5978 (t80) REVERT: A 187 MET cc_start: 0.9170 (mtp) cc_final: 0.8953 (mtm) REVERT: A 215 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 222 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: A 228 ASN cc_start: 0.8474 (m110) cc_final: 0.7859 (m-40) REVERT: A 258 TRP cc_start: 0.3459 (OUTLIER) cc_final: 0.2895 (t60) REVERT: A 288 LYS cc_start: 0.1187 (OUTLIER) cc_final: 0.0531 (pmtt) REVERT: A 318 LYS cc_start: 0.7687 (ptpt) cc_final: 0.7396 (pmmt) REVERT: A 436 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6489 (tttp) REVERT: A 501 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.6022 (mm-40) REVERT: A 682 VAL cc_start: 0.9090 (m) cc_final: 0.8768 (p) REVERT: B 47 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 85 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6916 (tpt170) REVERT: B 187 MET cc_start: 0.9179 (mtp) cc_final: 0.8962 (mtm) REVERT: B 215 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7927 (mm-30) REVERT: B 222 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: B 228 ASN cc_start: 0.8481 (m110) cc_final: 0.7849 (m-40) REVERT: B 258 TRP cc_start: 0.3466 (OUTLIER) cc_final: 0.2895 (t60) REVERT: B 288 LYS cc_start: 0.1183 (OUTLIER) cc_final: 0.0527 (pmtt) REVERT: B 318 LYS cc_start: 0.7696 (ptpt) cc_final: 0.7404 (pmmt) REVERT: B 436 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6506 (tttp) REVERT: B 501 GLN cc_start: 0.6415 (OUTLIER) cc_final: 0.6039 (mm-40) REVERT: B 682 VAL cc_start: 0.9086 (m) cc_final: 0.8759 (p) outliers start: 103 outliers final: 29 residues processed: 230 average time/residue: 0.4511 time to fit residues: 113.1285 Evaluate side-chains 168 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 654 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 208 ASN A 476 ASN A 616 GLN A 710 GLN B 74 HIS B 208 ASN B 476 ASN B 616 GLN B 710 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120019 restraints weight = 11760.308| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.04 r_work: 0.3211 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11002 Z= 0.169 Angle : 0.696 10.049 14952 Z= 0.349 Chirality : 0.046 0.187 1678 Planarity : 0.006 0.054 1872 Dihedral : 8.355 58.942 1506 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.90 % Favored : 91.79 % Rotamer: Outliers : 7.48 % Allowed : 26.32 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.23), residues: 1316 helix: 0.77 (0.17), residues: 874 sheet: -2.76 (0.75), residues: 36 loop : -2.91 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 207 TYR 0.017 0.002 TYR A 43 PHE 0.019 0.002 PHE B 390 TRP 0.024 0.001 TRP B 625 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00389 (11002) covalent geometry : angle 0.69610 (14952) hydrogen bonds : bond 0.04418 ( 662) hydrogen bonds : angle 5.09563 ( 1962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 140 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8045 (mp) REVERT: A 85 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7017 (tpt170) REVERT: A 215 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8006 (mm-30) REVERT: A 222 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7814 (tp30) REVERT: A 228 ASN cc_start: 0.8615 (m110) cc_final: 0.8408 (m110) REVERT: A 254 LYS cc_start: 0.5625 (ttpt) cc_final: 0.5047 (tptt) REVERT: A 258 TRP cc_start: 0.3575 (OUTLIER) cc_final: 0.3038 (t60) REVERT: A 288 LYS cc_start: 0.1150 (OUTLIER) cc_final: 0.0318 (pmtt) REVERT: A 295 TYR cc_start: 0.5930 (OUTLIER) cc_final: 0.5662 (m-80) REVERT: A 318 LYS cc_start: 0.7631 (ptpt) cc_final: 0.7386 (pmmt) REVERT: A 435 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6330 (mt) REVERT: A 524 ASP cc_start: 0.8112 (t70) cc_final: 0.7882 (t70) REVERT: A 560 MET cc_start: 0.6027 (ptm) cc_final: 0.5701 (ptp) REVERT: A 682 VAL cc_start: 0.9125 (m) cc_final: 0.8857 (p) REVERT: B 47 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 85 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7010 (tpt170) REVERT: B 215 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8037 (mm-30) REVERT: B 222 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7808 (tp30) REVERT: B 228 ASN cc_start: 0.8619 (m110) cc_final: 0.8414 (m110) REVERT: B 254 LYS cc_start: 0.5604 (ttpt) cc_final: 0.5044 (tptt) REVERT: B 258 TRP cc_start: 0.3578 (OUTLIER) cc_final: 0.3041 (t60) REVERT: B 288 LYS cc_start: 0.1138 (OUTLIER) cc_final: 0.0315 (pmtt) REVERT: B 295 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.5657 (m-80) REVERT: B 318 LYS cc_start: 0.7653 (ptpt) cc_final: 0.7410 (pmmt) REVERT: B 435 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6305 (mt) REVERT: B 524 ASP cc_start: 0.8123 (t70) cc_final: 0.7895 (t70) REVERT: B 560 MET cc_start: 0.6020 (ptm) cc_final: 0.5696 (ptp) REVERT: B 682 VAL cc_start: 0.9119 (m) cc_final: 0.8853 (p) outliers start: 85 outliers final: 38 residues processed: 205 average time/residue: 0.4701 time to fit residues: 104.7367 Evaluate side-chains 172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 128 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 500 ASN A 616 GLN B 74 HIS B 500 ASN B 616 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124263 restraints weight = 11873.004| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.15 r_work: 0.3197 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11002 Z= 0.145 Angle : 0.657 8.202 14952 Z= 0.325 Chirality : 0.045 0.301 1678 Planarity : 0.005 0.051 1872 Dihedral : 7.503 59.855 1500 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.67 % Favored : 92.02 % Rotamer: Outliers : 6.87 % Allowed : 28.08 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.24), residues: 1316 helix: 1.09 (0.18), residues: 862 sheet: -2.45 (0.76), residues: 36 loop : -2.79 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 197 TYR 0.014 0.001 TYR B 295 PHE 0.016 0.001 PHE B 390 TRP 0.022 0.001 TRP B 625 HIS 0.002 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00334 (11002) covalent geometry : angle 0.65688 (14952) hydrogen bonds : bond 0.04077 ( 662) hydrogen bonds : angle 4.89895 ( 1962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 131 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8058 (mp) REVERT: A 85 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6924 (tpt170) REVERT: A 215 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8027 (mm-30) REVERT: A 219 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: A 222 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7789 (tp30) REVERT: A 228 ASN cc_start: 0.8598 (m110) cc_final: 0.8335 (m110) REVERT: A 254 LYS cc_start: 0.5620 (ttpt) cc_final: 0.5051 (tttt) REVERT: A 258 TRP cc_start: 0.3575 (OUTLIER) cc_final: 0.3061 (t60) REVERT: A 288 LYS cc_start: 0.1273 (OUTLIER) cc_final: 0.0428 (pmtt) REVERT: A 295 TYR cc_start: 0.5910 (OUTLIER) cc_final: 0.5598 (m-80) REVERT: A 524 ASP cc_start: 0.8112 (t70) cc_final: 0.7838 (t70) REVERT: A 560 MET cc_start: 0.6070 (ptm) cc_final: 0.5781 (ptp) REVERT: A 682 VAL cc_start: 0.9095 (m) cc_final: 0.8794 (p) REVERT: B 47 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 85 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6923 (tpt170) REVERT: B 215 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8044 (mm-30) REVERT: B 219 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: B 222 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: B 228 ASN cc_start: 0.8610 (m110) cc_final: 0.8349 (m110) REVERT: B 254 LYS cc_start: 0.5605 (ttpt) cc_final: 0.5053 (tttt) REVERT: B 258 TRP cc_start: 0.3585 (OUTLIER) cc_final: 0.3068 (t60) REVERT: B 288 LYS cc_start: 0.1261 (OUTLIER) cc_final: 0.0424 (pmtt) REVERT: B 295 TYR cc_start: 0.5900 (OUTLIER) cc_final: 0.5592 (m-80) REVERT: B 436 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6740 (tttp) REVERT: B 524 ASP cc_start: 0.8127 (t70) cc_final: 0.7856 (t70) REVERT: B 560 MET cc_start: 0.6061 (ptm) cc_final: 0.5779 (ptp) REVERT: B 682 VAL cc_start: 0.9090 (m) cc_final: 0.8786 (p) outliers start: 78 outliers final: 40 residues processed: 185 average time/residue: 0.4476 time to fit residues: 90.4607 Evaluate side-chains 170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 208 ASN A 616 GLN B 74 HIS B 208 ASN B 616 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.179003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120220 restraints weight = 11804.168| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.50 r_work: 0.3131 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11002 Z= 0.162 Angle : 0.659 7.971 14952 Z= 0.326 Chirality : 0.046 0.302 1678 Planarity : 0.005 0.049 1872 Dihedral : 7.100 59.216 1498 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 6.87 % Allowed : 27.38 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.24), residues: 1316 helix: 1.09 (0.17), residues: 874 sheet: -2.25 (0.79), residues: 36 loop : -2.70 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.015 0.001 TYR B 295 PHE 0.015 0.001 PHE A 390 TRP 0.021 0.001 TRP B 625 HIS 0.003 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00385 (11002) covalent geometry : angle 0.65859 (14952) hydrogen bonds : bond 0.04149 ( 662) hydrogen bonds : angle 4.84934 ( 1962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 129 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 85 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6953 (tpt170) REVERT: A 215 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8092 (mm-30) REVERT: A 222 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: A 240 CYS cc_start: 0.8604 (p) cc_final: 0.8396 (p) REVERT: A 254 LYS cc_start: 0.5586 (ttpt) cc_final: 0.5056 (tttt) REVERT: A 258 TRP cc_start: 0.3576 (OUTLIER) cc_final: 0.3082 (t60) REVERT: A 318 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7333 (pmmt) REVERT: A 524 ASP cc_start: 0.8165 (t70) cc_final: 0.7899 (t70) REVERT: A 682 VAL cc_start: 0.9121 (m) cc_final: 0.8838 (p) REVERT: B 47 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8072 (mp) REVERT: B 85 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6945 (tpt170) REVERT: B 215 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8109 (mm-30) REVERT: B 222 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: B 240 CYS cc_start: 0.8606 (p) cc_final: 0.8396 (p) REVERT: B 254 LYS cc_start: 0.5607 (ttpt) cc_final: 0.5057 (tttt) REVERT: B 258 TRP cc_start: 0.3586 (OUTLIER) cc_final: 0.3084 (t60) REVERT: B 318 LYS cc_start: 0.7611 (ptpt) cc_final: 0.7333 (pmmt) REVERT: B 436 LYS cc_start: 0.6908 (tttt) cc_final: 0.6655 (tttp) REVERT: B 524 ASP cc_start: 0.8178 (t70) cc_final: 0.7913 (t70) REVERT: B 682 VAL cc_start: 0.9118 (m) cc_final: 0.8833 (p) outliers start: 78 outliers final: 38 residues processed: 191 average time/residue: 0.4608 time to fit residues: 95.9796 Evaluate side-chains 167 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 43 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 0.0670 chunk 71 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 74 HIS A 228 ASN A 616 GLN B 14 ASN B 74 HIS B 228 ASN B 616 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.181676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127604 restraints weight = 11763.360| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.10 r_work: 0.3155 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11002 Z= 0.137 Angle : 0.631 8.002 14952 Z= 0.311 Chirality : 0.044 0.290 1678 Planarity : 0.005 0.049 1872 Dihedral : 6.655 58.268 1490 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.29 % Favored : 92.40 % Rotamer: Outliers : 5.81 % Allowed : 28.43 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.24), residues: 1316 helix: 1.23 (0.18), residues: 874 sheet: -2.04 (0.83), residues: 36 loop : -2.68 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.012 0.001 TYR A 295 PHE 0.013 0.001 PHE A 390 TRP 0.021 0.001 TRP B 625 HIS 0.003 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00321 (11002) covalent geometry : angle 0.63126 (14952) hydrogen bonds : bond 0.03833 ( 662) hydrogen bonds : angle 4.79028 ( 1962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 135 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7001 (tpt170) REVERT: A 182 GLU cc_start: 0.8761 (tt0) cc_final: 0.7999 (tt0) REVERT: A 222 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: A 240 CYS cc_start: 0.8612 (p) cc_final: 0.8400 (p) REVERT: A 254 LYS cc_start: 0.5693 (ttpt) cc_final: 0.5082 (tttt) REVERT: A 258 TRP cc_start: 0.3598 (OUTLIER) cc_final: 0.3065 (t60) REVERT: A 288 LYS cc_start: 0.1416 (OUTLIER) cc_final: 0.0672 (pmtt) REVERT: A 385 PHE cc_start: 0.7940 (m-80) cc_final: 0.7498 (m-80) REVERT: A 430 LEU cc_start: 0.2525 (OUTLIER) cc_final: 0.2160 (mp) REVERT: A 508 MET cc_start: 0.6569 (mtp) cc_final: 0.6222 (mpp) REVERT: A 524 ASP cc_start: 0.8220 (t70) cc_final: 0.7943 (t70) REVERT: A 682 VAL cc_start: 0.9124 (m) cc_final: 0.8811 (p) REVERT: B 85 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6993 (tpt170) REVERT: B 182 GLU cc_start: 0.8757 (tt0) cc_final: 0.7989 (tt0) REVERT: B 222 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: B 240 CYS cc_start: 0.8620 (p) cc_final: 0.8409 (p) REVERT: B 254 LYS cc_start: 0.5689 (ttpt) cc_final: 0.5081 (tttt) REVERT: B 258 TRP cc_start: 0.3592 (OUTLIER) cc_final: 0.3057 (t60) REVERT: B 288 LYS cc_start: 0.1416 (OUTLIER) cc_final: 0.0672 (pmtt) REVERT: B 385 PHE cc_start: 0.7938 (m-80) cc_final: 0.7507 (m-80) REVERT: B 430 LEU cc_start: 0.2505 (OUTLIER) cc_final: 0.2151 (mp) REVERT: B 508 MET cc_start: 0.6563 (mtp) cc_final: 0.6206 (mpp) REVERT: B 524 ASP cc_start: 0.8220 (t70) cc_final: 0.7944 (t70) REVERT: B 682 VAL cc_start: 0.9125 (m) cc_final: 0.8803 (p) outliers start: 66 outliers final: 32 residues processed: 186 average time/residue: 0.4985 time to fit residues: 100.3829 Evaluate side-chains 165 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 616 GLN B 74 HIS B 616 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.178203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124616 restraints weight = 11714.001| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.07 r_work: 0.3142 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11002 Z= 0.142 Angle : 0.631 8.230 14952 Z= 0.312 Chirality : 0.044 0.302 1678 Planarity : 0.005 0.048 1872 Dihedral : 6.507 57.716 1488 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.07 % Favored : 92.63 % Rotamer: Outliers : 4.84 % Allowed : 28.96 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.24), residues: 1316 helix: 1.31 (0.17), residues: 874 sheet: -2.00 (0.84), residues: 36 loop : -2.66 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.010 0.001 TYR A 577 PHE 0.012 0.001 PHE A 390 TRP 0.019 0.001 TRP A 625 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00334 (11002) covalent geometry : angle 0.63144 (14952) hydrogen bonds : bond 0.03854 ( 662) hydrogen bonds : angle 4.72139 ( 1962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8739 (tt0) cc_final: 0.7976 (tt0) REVERT: A 222 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7849 (tp30) REVERT: A 254 LYS cc_start: 0.5738 (ttpt) cc_final: 0.5134 (tttt) REVERT: A 258 TRP cc_start: 0.3609 (OUTLIER) cc_final: 0.3117 (t60) REVERT: A 318 LYS cc_start: 0.7585 (ptpt) cc_final: 0.7366 (pmmt) REVERT: A 385 PHE cc_start: 0.7934 (m-80) cc_final: 0.7473 (m-80) REVERT: A 430 LEU cc_start: 0.2440 (OUTLIER) cc_final: 0.2163 (mp) REVERT: A 524 ASP cc_start: 0.8279 (t70) cc_final: 0.7988 (t70) REVERT: A 682 VAL cc_start: 0.9111 (m) cc_final: 0.8777 (p) REVERT: B 182 GLU cc_start: 0.8745 (tt0) cc_final: 0.7984 (tt0) REVERT: B 222 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: B 254 LYS cc_start: 0.5718 (ttpt) cc_final: 0.5119 (tttt) REVERT: B 258 TRP cc_start: 0.3608 (OUTLIER) cc_final: 0.3116 (t60) REVERT: B 318 LYS cc_start: 0.7588 (ptpt) cc_final: 0.7372 (pmmt) REVERT: B 385 PHE cc_start: 0.7947 (m-80) cc_final: 0.7449 (m-80) REVERT: B 430 LEU cc_start: 0.2467 (OUTLIER) cc_final: 0.2189 (mp) REVERT: B 524 ASP cc_start: 0.8286 (t70) cc_final: 0.7998 (t70) REVERT: B 682 VAL cc_start: 0.9112 (m) cc_final: 0.8779 (p) outliers start: 55 outliers final: 28 residues processed: 167 average time/residue: 0.4640 time to fit residues: 84.3060 Evaluate side-chains 153 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 44 optimal weight: 0.2980 chunk 115 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 208 ASN A 616 GLN B 74 HIS B 208 ASN B 616 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123890 restraints weight = 11678.204| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.12 r_work: 0.3131 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11002 Z= 0.148 Angle : 0.643 8.814 14952 Z= 0.317 Chirality : 0.045 0.312 1678 Planarity : 0.005 0.047 1872 Dihedral : 5.968 57.139 1480 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 4.14 % Allowed : 30.37 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.24), residues: 1316 helix: 1.33 (0.17), residues: 878 sheet: -1.98 (0.84), residues: 36 loop : -2.57 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.010 0.001 TYR B 542 PHE 0.011 0.001 PHE B 598 TRP 0.019 0.001 TRP B 625 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00351 (11002) covalent geometry : angle 0.64279 (14952) hydrogen bonds : bond 0.03856 ( 662) hydrogen bonds : angle 4.71738 ( 1962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8781 (tt0) cc_final: 0.8043 (tt0) REVERT: A 222 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: A 254 LYS cc_start: 0.5717 (ttpt) cc_final: 0.5145 (tttt) REVERT: A 258 TRP cc_start: 0.3657 (OUTLIER) cc_final: 0.3138 (t60) REVERT: A 318 LYS cc_start: 0.7533 (ptpt) cc_final: 0.7317 (pmmt) REVERT: A 385 PHE cc_start: 0.8001 (m-80) cc_final: 0.7557 (m-80) REVERT: A 430 LEU cc_start: 0.2379 (OUTLIER) cc_final: 0.2172 (mp) REVERT: A 508 MET cc_start: 0.6598 (mtp) cc_final: 0.6279 (mpp) REVERT: A 524 ASP cc_start: 0.8253 (t70) cc_final: 0.7962 (t70) REVERT: A 682 VAL cc_start: 0.9147 (m) cc_final: 0.8855 (p) REVERT: B 182 GLU cc_start: 0.8769 (tt0) cc_final: 0.8026 (tt0) REVERT: B 222 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: B 254 LYS cc_start: 0.5728 (ttpt) cc_final: 0.5146 (tttt) REVERT: B 258 TRP cc_start: 0.3662 (OUTLIER) cc_final: 0.3139 (t60) REVERT: B 385 PHE cc_start: 0.8004 (m-80) cc_final: 0.7524 (m-80) REVERT: B 508 MET cc_start: 0.6608 (mtp) cc_final: 0.6287 (mpp) REVERT: B 524 ASP cc_start: 0.8258 (t70) cc_final: 0.7969 (t70) REVERT: B 682 VAL cc_start: 0.9150 (m) cc_final: 0.8847 (p) outliers start: 47 outliers final: 25 residues processed: 164 average time/residue: 0.4088 time to fit residues: 73.7046 Evaluate side-chains 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 129 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 616 GLN B 74 HIS B 616 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120298 restraints weight = 11691.517| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.03 r_work: 0.3122 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11002 Z= 0.146 Angle : 0.639 9.236 14952 Z= 0.315 Chirality : 0.045 0.334 1678 Planarity : 0.005 0.047 1872 Dihedral : 5.630 56.418 1466 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.14 % Favored : 92.55 % Rotamer: Outliers : 3.87 % Allowed : 30.11 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.24), residues: 1316 helix: 1.36 (0.17), residues: 878 sheet: -1.91 (0.84), residues: 36 loop : -2.52 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.010 0.001 TYR B 542 PHE 0.012 0.001 PHE A 390 TRP 0.020 0.001 TRP A 625 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00346 (11002) covalent geometry : angle 0.63916 (14952) hydrogen bonds : bond 0.03822 ( 662) hydrogen bonds : angle 4.66925 ( 1962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8758 (tt0) cc_final: 0.8031 (tt0) REVERT: A 222 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: A 254 LYS cc_start: 0.5652 (ttpt) cc_final: 0.5131 (tttt) REVERT: A 258 TRP cc_start: 0.3644 (OUTLIER) cc_final: 0.3140 (t60) REVERT: A 318 LYS cc_start: 0.7554 (ptpt) cc_final: 0.7354 (pmmt) REVERT: A 385 PHE cc_start: 0.7973 (m-80) cc_final: 0.7516 (m-80) REVERT: A 508 MET cc_start: 0.6659 (mtp) cc_final: 0.6321 (mpp) REVERT: A 524 ASP cc_start: 0.8238 (t70) cc_final: 0.7953 (t70) REVERT: A 560 MET cc_start: 0.6305 (ptm) cc_final: 0.6000 (ttp) REVERT: A 682 VAL cc_start: 0.9124 (m) cc_final: 0.8849 (p) REVERT: B 182 GLU cc_start: 0.8753 (tt0) cc_final: 0.8020 (tt0) REVERT: B 222 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: B 254 LYS cc_start: 0.5679 (ttpt) cc_final: 0.5146 (tttt) REVERT: B 258 TRP cc_start: 0.3649 (OUTLIER) cc_final: 0.3146 (t60) REVERT: B 318 LYS cc_start: 0.7560 (ptpt) cc_final: 0.7359 (pmmt) REVERT: B 385 PHE cc_start: 0.7970 (m-80) cc_final: 0.7511 (m-80) REVERT: B 508 MET cc_start: 0.6657 (mtp) cc_final: 0.6316 (mpp) REVERT: B 524 ASP cc_start: 0.8233 (t70) cc_final: 0.7947 (t70) REVERT: B 560 MET cc_start: 0.6291 (ptm) cc_final: 0.5991 (ttp) REVERT: B 682 VAL cc_start: 0.9130 (m) cc_final: 0.8848 (p) outliers start: 44 outliers final: 28 residues processed: 158 average time/residue: 0.4368 time to fit residues: 75.6138 Evaluate side-chains 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 616 GLN B 74 HIS B 616 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119885 restraints weight = 11692.042| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.05 r_work: 0.3122 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11002 Z= 0.146 Angle : 0.636 9.374 14952 Z= 0.313 Chirality : 0.045 0.339 1678 Planarity : 0.005 0.047 1872 Dihedral : 5.561 55.815 1466 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.07 % Favored : 92.63 % Rotamer: Outliers : 3.17 % Allowed : 30.55 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.24), residues: 1316 helix: 1.41 (0.17), residues: 876 sheet: -1.90 (0.83), residues: 36 loop : -2.50 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.011 0.001 TYR A 542 PHE 0.012 0.001 PHE A 390 TRP 0.020 0.001 TRP A 625 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00346 (11002) covalent geometry : angle 0.63637 (14952) hydrogen bonds : bond 0.03802 ( 662) hydrogen bonds : angle 4.65874 ( 1962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8756 (tt0) cc_final: 0.8029 (tt0) REVERT: A 222 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: A 254 LYS cc_start: 0.5633 (ttpt) cc_final: 0.5145 (tttt) REVERT: A 258 TRP cc_start: 0.3589 (OUTLIER) cc_final: 0.3100 (t60) REVERT: A 318 LYS cc_start: 0.7521 (ptpt) cc_final: 0.7320 (pmmt) REVERT: A 385 PHE cc_start: 0.7997 (m-80) cc_final: 0.7529 (m-80) REVERT: A 508 MET cc_start: 0.6659 (mtp) cc_final: 0.6327 (mpp) REVERT: A 524 ASP cc_start: 0.8246 (t70) cc_final: 0.7961 (t70) REVERT: A 560 MET cc_start: 0.6335 (ptm) cc_final: 0.6018 (ttp) REVERT: A 682 VAL cc_start: 0.9127 (m) cc_final: 0.8850 (p) REVERT: B 182 GLU cc_start: 0.8750 (tt0) cc_final: 0.8019 (tt0) REVERT: B 222 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: B 254 LYS cc_start: 0.5677 (ttpt) cc_final: 0.5154 (tttt) REVERT: B 258 TRP cc_start: 0.3616 (OUTLIER) cc_final: 0.3096 (t60) REVERT: B 385 PHE cc_start: 0.7999 (m-80) cc_final: 0.7525 (m-80) REVERT: B 508 MET cc_start: 0.6645 (mtp) cc_final: 0.6305 (mpp) REVERT: B 524 ASP cc_start: 0.8245 (t70) cc_final: 0.7961 (t70) REVERT: B 560 MET cc_start: 0.6319 (ptm) cc_final: 0.6013 (ttp) REVERT: B 682 VAL cc_start: 0.9130 (m) cc_final: 0.8848 (p) outliers start: 36 outliers final: 22 residues processed: 149 average time/residue: 0.4478 time to fit residues: 72.8354 Evaluate side-chains 145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 0.4980 chunk 44 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 616 GLN B 74 HIS B 616 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.181793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121840 restraints weight = 11679.052| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.04 r_work: 0.3185 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11002 Z= 0.132 Angle : 0.618 9.233 14952 Z= 0.305 Chirality : 0.044 0.333 1678 Planarity : 0.005 0.047 1872 Dihedral : 5.240 54.953 1462 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.45 % Favored : 92.25 % Rotamer: Outliers : 2.73 % Allowed : 30.63 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.24), residues: 1316 helix: 1.51 (0.17), residues: 866 sheet: -1.78 (0.85), residues: 36 loop : -2.45 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.009 0.001 TYR B 577 PHE 0.012 0.001 PHE A 390 TRP 0.020 0.001 TRP A 625 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00310 (11002) covalent geometry : angle 0.61773 (14952) hydrogen bonds : bond 0.03642 ( 662) hydrogen bonds : angle 4.59503 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5604.93 seconds wall clock time: 96 minutes 6.39 seconds (5766.39 seconds total)