Starting phenix.real_space_refine on Sat Aug 23 01:59:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k13_36785/08_2025/8k13_36785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k13_36785/08_2025/8k13_36785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k13_36785/08_2025/8k13_36785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k13_36785/08_2025/8k13_36785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k13_36785/08_2025/8k13_36785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k13_36785/08_2025/8k13_36785.map" } resolution = 3.33 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= 0.007 sd= 0.126 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 54 5.16 5 C 6004 2.51 5 N 1424 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9078 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4497 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 537} Chain breaks: 5 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4497 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 537} Chain breaks: 5 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.37, per 1000 atoms: 0.26 Number of scatterers: 9078 At special positions: 0 Unit cell: (93.15, 79.65, 117.45, 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 54 16.00 O 1596 8.00 N 1424 7.00 C 6004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 782 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 67 " " NAG A 902 " - " ASN A 83 " " NAG A 903 " - " ASN A 136 " " NAG B 901 " - " ASN B 67 " " NAG B 902 " - " ASN B 83 " " NAG B 903 " - " ASN B 136 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 368.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 47.3% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 333 removed outlier: 3.747A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 474 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.044A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 524 removed outlier: 3.632A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 4.195A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 586 removed outlier: 3.535A pdb=" N PHE A 571 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 644 removed outlier: 3.792A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 Processing helix chain 'A' and resid 708 through 734 removed outlier: 3.508A pdb=" N TYR A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 762 removed outlier: 3.941A pdb=" N ALA A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.966A pdb=" N LYS A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 809 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 302 through 333 removed outlier: 3.823A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 474 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 4.112A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 524 removed outlier: 3.608A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 4.357A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 586 removed outlier: 3.971A pdb=" N GLN B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 644 removed outlier: 3.822A pdb=" N SER B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 705 removed outlier: 3.523A pdb=" N PHE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 735 Processing helix chain 'B' and resid 744 through 762 removed outlier: 4.019A pdb=" N ALA B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 752 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 776 Processing helix chain 'B' and resid 789 through 809 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 56 removed outlier: 4.274A pdb=" N HIS A 50 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 163 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 removed outlier: 3.836A pdb=" N SER A 70 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 141 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 removed outlier: 7.497A pdb=" N SER A 119 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 56 removed outlier: 4.047A pdb=" N HIS B 50 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 163 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 56 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 70 removed outlier: 3.878A pdb=" N SER B 70 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 141 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113 removed outlier: 3.850A pdb=" N PHE B 112 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER B 119 " --> pdb=" O GLN B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 171 removed outlier: 4.939A pdb=" N LYS B 192 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 177 through 181 532 hydrogen bonds defined for protein. 1536 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: 1.60 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2732 1.34 - 1.46: 2496 1.46 - 1.58: 4014 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9324 Sorted by residual: bond pdb=" N ASN A 121 " pdb=" CA ASN A 121 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.20e-02 6.94e+03 5.82e+00 bond pdb=" N TYR A 64 " pdb=" CA TYR A 64 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.53e+00 bond pdb=" N ASN B 230 " pdb=" CA ASN B 230 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.40e-02 5.10e+03 5.50e+00 bond pdb=" C TYR A 120 " pdb=" N ASN A 121 " ideal model delta sigma weight residual 1.331 1.365 -0.034 1.44e-02 4.82e+03 5.48e+00 bond pdb=" N ASN A 230 " pdb=" CA ASN A 230 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.40e-02 5.10e+03 5.43e+00 ... (remaining 9319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 12328 1.54 - 3.08: 284 3.08 - 4.63: 57 4.63 - 6.17: 8 6.17 - 7.71: 5 Bond angle restraints: 12682 Sorted by residual: angle pdb=" N PHE A 320 " pdb=" CA PHE A 320 " pdb=" C PHE A 320 " ideal model delta sigma weight residual 111.36 107.12 4.24 1.09e+00 8.42e-01 1.51e+01 angle pdb=" C ASN A 230 " pdb=" CA ASN A 230 " pdb=" CB ASN A 230 " ideal model delta sigma weight residual 109.13 114.87 -5.74 1.56e+00 4.11e-01 1.36e+01 angle pdb=" C ASN B 230 " pdb=" CA ASN B 230 " pdb=" CB ASN B 230 " ideal model delta sigma weight residual 109.13 114.86 -5.73 1.56e+00 4.11e-01 1.35e+01 angle pdb=" CA ASN A 219 " pdb=" C ASN A 219 " pdb=" O ASN A 219 " ideal model delta sigma weight residual 121.94 118.53 3.41 1.15e+00 7.56e-01 8.77e+00 angle pdb=" CA ASN B 219 " pdb=" C ASN B 219 " pdb=" O ASN B 219 " ideal model delta sigma weight residual 121.94 118.59 3.35 1.15e+00 7.56e-01 8.47e+00 ... (remaining 12677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4663 17.31 - 34.62: 646 34.62 - 51.94: 172 51.94 - 69.25: 18 69.25 - 86.56: 5 Dihedral angle restraints: 5504 sinusoidal: 2186 harmonic: 3318 Sorted by residual: dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 56.85 36.15 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CA GLN B 117 " pdb=" C GLN B 117 " pdb=" N ARG B 118 " pdb=" CA ARG B 118 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CB CYS B 212 " pdb=" SG CYS B 212 " pdb=" SG CYS B 271 " pdb=" CB CYS B 271 " ideal model delta sinusoidal sigma weight residual 93.00 61.07 31.93 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 5501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1087 0.045 - 0.090: 275 0.090 - 0.135: 93 0.135 - 0.180: 6 0.180 - 0.226: 1 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CB ILE A 316 " pdb=" CA ILE A 316 " pdb=" CG1 ILE A 316 " pdb=" CG2 ILE A 316 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASN B 764 " pdb=" N ASN B 764 " pdb=" C ASN B 764 " pdb=" CB ASN B 764 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA TYR B 64 " pdb=" N TYR B 64 " pdb=" C TYR B 64 " pdb=" CB TYR B 64 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 1459 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 222 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 223 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 222 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 223 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 229 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C HIS A 229 " -0.029 2.00e-02 2.50e+03 pdb=" O HIS A 229 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 230 " 0.010 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 804 2.74 - 3.28: 9209 3.28 - 3.82: 14827 3.82 - 4.36: 16508 4.36 - 4.90: 29053 Nonbonded interactions: 70401 Sorted by model distance: nonbonded pdb=" O VAL A 469 " pdb=" OG1 THR A 473 " model vdw 2.205 3.040 nonbonded pdb=" O SER A 239 " pdb=" NH1 ARG A 776 " model vdw 2.209 3.120 nonbonded pdb=" O GLU B 124 " pdb=" OG SER B 184 " model vdw 2.209 3.040 nonbonded pdb=" O SER B 239 " pdb=" NH1 ARG B 776 " model vdw 2.213 3.120 nonbonded pdb=" O VAL B 469 " pdb=" OG1 THR B 473 " model vdw 2.215 3.040 ... (remaining 70396 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: 0.300 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.140 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 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 : 0.003 0.041 9338 Z= 0.179 Angle : 0.594 7.712 12716 Z= 0.330 Chirality : 0.043 0.226 1462 Planarity : 0.003 0.049 1560 Dihedral : 16.509 86.562 3332 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.40 % Allowed : 26.06 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.67 (0.25), residues: 1094 helix: 1.90 (0.23), residues: 480 sheet: 0.59 (0.32), residues: 256 loop : -1.74 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 289 TYR 0.013 0.001 TYR B 269 PHE 0.014 0.001 PHE A 727 TRP 0.005 0.001 TRP A 695 HIS 0.005 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9324) covalent geometry : angle 0.58443 (12682) SS BOND : bond 0.00188 ( 8) SS BOND : angle 1.25263 ( 16) hydrogen bonds : bond 0.16691 ( 532) hydrogen bonds : angle 6.76235 ( 1536) link_NAG-ASN : bond 0.00293 ( 6) link_NAG-ASN : angle 2.63909 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.7758 (t80) cc_final: 0.7409 (t80) REVERT: A 681 MET cc_start: 0.3968 (mmp) cc_final: 0.2308 (ttt) REVERT: A 684 MET cc_start: -0.0279 (mmt) cc_final: -0.0763 (pmm) REVERT: B 116 TYR cc_start: 0.8204 (m-80) cc_final: 0.7596 (m-10) REVERT: B 455 TYR cc_start: 0.7983 (t80) cc_final: 0.7350 (t80) REVERT: B 485 CYS cc_start: 0.6209 (t) cc_final: 0.5685 (t) REVERT: B 575 THR cc_start: 0.8078 (p) cc_final: 0.7800 (t) REVERT: B 681 MET cc_start: 0.3850 (mmp) cc_final: 0.2283 (ttm) REVERT: B 684 MET cc_start: -0.0169 (mmt) cc_final: -0.0442 (pmm) outliers start: 4 outliers final: 0 residues processed: 212 average time/residue: 0.0864 time to fit residues: 26.4585 Evaluate side-chains 146 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.0060 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 501 ASN B 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.213350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.158813 restraints weight = 11730.910| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 4.08 r_work: 0.3811 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 9338 Z= 0.211 Angle : 0.648 8.170 12716 Z= 0.337 Chirality : 0.046 0.146 1462 Planarity : 0.005 0.050 1560 Dihedral : 6.300 55.285 1324 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.05 % Allowed : 24.14 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.84 (0.26), residues: 1094 helix: 2.22 (0.23), residues: 484 sheet: 0.33 (0.33), residues: 248 loop : -1.64 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 776 TYR 0.025 0.002 TYR A 188 PHE 0.014 0.002 PHE B 796 TRP 0.022 0.002 TRP B 629 HIS 0.003 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9324) covalent geometry : angle 0.63918 (12682) SS BOND : bond 0.00366 ( 8) SS BOND : angle 1.37341 ( 16) hydrogen bonds : bond 0.04528 ( 532) hydrogen bonds : angle 5.23842 ( 1536) link_NAG-ASN : bond 0.00309 ( 6) link_NAG-ASN : angle 2.74807 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7898 (t0) REVERT: A 316 ILE cc_start: 0.8438 (pp) cc_final: 0.8199 (pp) REVERT: A 455 TYR cc_start: 0.8044 (t80) cc_final: 0.7610 (t80) REVERT: A 578 MET cc_start: 0.2707 (ttt) cc_final: 0.2464 (mtp) REVERT: A 580 MET cc_start: 0.5832 (mtt) cc_final: 0.5398 (mtt) REVERT: A 681 MET cc_start: 0.3538 (mmp) cc_final: 0.1696 (ttm) REVERT: A 684 MET cc_start: -0.0626 (mmt) cc_final: -0.1101 (pmm) REVERT: A 759 TYR cc_start: 0.7841 (t80) cc_final: 0.7487 (t80) REVERT: B 106 TRP cc_start: 0.8027 (p90) cc_final: 0.7681 (p90) REVERT: B 117 GLN cc_start: 0.7713 (pp30) cc_final: 0.7276 (pp30) REVERT: B 325 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6843 (pp) REVERT: B 455 TYR cc_start: 0.8168 (t80) cc_final: 0.7852 (t80) REVERT: B 517 ARG cc_start: 0.7399 (tpt170) cc_final: 0.7091 (ptm-80) REVERT: B 548 MET cc_start: 0.7684 (mmt) cc_final: 0.7484 (ptp) REVERT: B 555 GLU cc_start: 0.8791 (tm-30) cc_final: 0.7901 (tp30) REVERT: B 681 MET cc_start: 0.3299 (mmp) cc_final: 0.1449 (ttm) REVERT: B 684 MET cc_start: -0.0638 (mmt) cc_final: -0.1066 (pmm) REVERT: B 727 PHE cc_start: 0.7817 (m-10) cc_final: 0.7341 (m-10) REVERT: B 731 MET cc_start: 0.7891 (mmm) cc_final: 0.7179 (ttt) REVERT: B 769 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: B 778 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8708 (mttm) REVERT: B 804 PHE cc_start: 0.7963 (m-80) cc_final: 0.7739 (m-80) outliers start: 50 outliers final: 25 residues processed: 182 average time/residue: 0.0710 time to fit residues: 19.6231 Evaluate side-chains 160 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 778 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 51 optimal weight: 0.0670 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.216542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.163885 restraints weight = 11638.395| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.66 r_work: 0.3904 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9338 Z= 0.138 Angle : 0.580 10.901 12716 Z= 0.296 Chirality : 0.044 0.146 1462 Planarity : 0.004 0.047 1560 Dihedral : 5.982 58.241 1324 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.04 % Allowed : 23.64 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.02 (0.26), residues: 1094 helix: 2.44 (0.23), residues: 482 sheet: 0.43 (0.33), residues: 240 loop : -1.63 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 776 TYR 0.017 0.001 TYR A 188 PHE 0.022 0.001 PHE B 700 TRP 0.013 0.001 TRP B 629 HIS 0.007 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9324) covalent geometry : angle 0.57179 (12682) SS BOND : bond 0.00287 ( 8) SS BOND : angle 0.93423 ( 16) hydrogen bonds : bond 0.04073 ( 532) hydrogen bonds : angle 4.86607 ( 1536) link_NAG-ASN : bond 0.00246 ( 6) link_NAG-ASN : angle 2.58648 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7631 (pt) cc_final: 0.7420 (pp) REVERT: A 316 ILE cc_start: 0.8410 (pp) cc_final: 0.8206 (pp) REVERT: A 455 TYR cc_start: 0.8156 (t80) cc_final: 0.7338 (t80) REVERT: A 578 MET cc_start: 0.2696 (ttt) cc_final: 0.2396 (mtp) REVERT: A 580 MET cc_start: 0.5786 (mtt) cc_final: 0.5342 (mtt) REVERT: A 681 MET cc_start: 0.3520 (mmp) cc_final: 0.2226 (ttm) REVERT: A 684 MET cc_start: -0.0422 (mmt) cc_final: -0.0950 (ptp) REVERT: B 111 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7128 (tt) REVERT: B 117 GLN cc_start: 0.7695 (pp30) cc_final: 0.7271 (pp30) REVERT: B 325 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6868 (pp) REVERT: B 451 ILE cc_start: 0.8224 (mm) cc_final: 0.7987 (pt) REVERT: B 455 TYR cc_start: 0.8181 (t80) cc_final: 0.7829 (t80) REVERT: B 517 ARG cc_start: 0.7397 (tpt170) cc_final: 0.7075 (ptm-80) REVERT: B 555 GLU cc_start: 0.8742 (tm-30) cc_final: 0.7946 (tp30) REVERT: B 580 MET cc_start: 0.5396 (mtt) cc_final: 0.5103 (mtt) REVERT: B 681 MET cc_start: 0.3354 (mmp) cc_final: 0.1961 (mtp) REVERT: B 684 MET cc_start: -0.0655 (mmt) cc_final: -0.1153 (ptp) REVERT: B 727 PHE cc_start: 0.7808 (m-10) cc_final: 0.7414 (m-10) REVERT: B 731 MET cc_start: 0.8205 (mmm) cc_final: 0.7309 (ttt) REVERT: B 753 MET cc_start: 0.8596 (mmp) cc_final: 0.8389 (mmm) REVERT: B 778 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8724 (mttm) outliers start: 40 outliers final: 22 residues processed: 181 average time/residue: 0.0753 time to fit residues: 20.9378 Evaluate side-chains 164 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 778 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 91 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.216556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.163680 restraints weight = 11681.342| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 4.15 r_work: 0.3889 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9338 Z= 0.122 Angle : 0.553 8.330 12716 Z= 0.282 Chirality : 0.043 0.138 1462 Planarity : 0.003 0.047 1560 Dihedral : 5.362 49.750 1324 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.14 % Allowed : 23.74 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.02 (0.25), residues: 1094 helix: 2.49 (0.23), residues: 480 sheet: 0.41 (0.32), residues: 236 loop : -1.65 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.016 0.001 TYR A 188 PHE 0.021 0.001 PHE B 806 TRP 0.011 0.001 TRP B 629 HIS 0.002 0.000 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9324) covalent geometry : angle 0.54502 (12682) SS BOND : bond 0.00266 ( 8) SS BOND : angle 0.80256 ( 16) hydrogen bonds : bond 0.03853 ( 532) hydrogen bonds : angle 4.69610 ( 1536) link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 2.52987 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8162 (t80) cc_final: 0.7310 (t80) REVERT: A 578 MET cc_start: 0.2551 (ttt) cc_final: 0.2260 (mtp) REVERT: A 580 MET cc_start: 0.5754 (mtt) cc_final: 0.5259 (mtt) REVERT: A 681 MET cc_start: 0.3401 (mmp) cc_final: 0.1992 (ttm) REVERT: A 684 MET cc_start: -0.0623 (mmt) cc_final: -0.1195 (ptp) REVERT: A 727 PHE cc_start: 0.7802 (m-10) cc_final: 0.7472 (m-10) REVERT: A 731 MET cc_start: 0.8156 (mmm) cc_final: 0.7277 (ttt) REVERT: A 778 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8627 (mttm) REVERT: B 111 LEU cc_start: 0.7427 (mp) cc_final: 0.7103 (tt) REVERT: B 117 GLN cc_start: 0.7840 (pp30) cc_final: 0.7331 (pp30) REVERT: B 144 LEU cc_start: 0.7574 (pt) cc_final: 0.7370 (pp) REVERT: B 317 PHE cc_start: 0.7817 (m-80) cc_final: 0.7444 (m-80) REVERT: B 451 ILE cc_start: 0.8206 (mm) cc_final: 0.7981 (pt) REVERT: B 455 TYR cc_start: 0.8184 (t80) cc_final: 0.7591 (t80) REVERT: B 489 LEU cc_start: 0.8889 (tp) cc_final: 0.8550 (tp) REVERT: B 509 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7825 (t80) REVERT: B 517 ARG cc_start: 0.7304 (tpt170) cc_final: 0.6970 (ptm-80) REVERT: B 548 MET cc_start: 0.7766 (ptp) cc_final: 0.7293 (ptp) REVERT: B 555 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7845 (tp30) REVERT: B 580 MET cc_start: 0.5483 (mtt) cc_final: 0.5119 (mtt) REVERT: B 681 MET cc_start: 0.3409 (mmp) cc_final: 0.1981 (mtp) REVERT: B 684 MET cc_start: -0.0396 (mmt) cc_final: -0.0971 (ptp) REVERT: B 727 PHE cc_start: 0.7923 (m-10) cc_final: 0.7556 (m-10) REVERT: B 731 MET cc_start: 0.8299 (mmm) cc_final: 0.7387 (ttt) REVERT: B 806 PHE cc_start: 0.7364 (m-10) cc_final: 0.6908 (m-80) outliers start: 41 outliers final: 27 residues processed: 181 average time/residue: 0.0689 time to fit residues: 19.1006 Evaluate side-chains 168 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 476 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.208798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.152826 restraints weight = 11868.057| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 4.10 r_work: 0.3793 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 9338 Z= 0.241 Angle : 0.662 8.162 12716 Z= 0.342 Chirality : 0.047 0.152 1462 Planarity : 0.005 0.052 1560 Dihedral : 5.457 50.391 1324 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.25 % Allowed : 24.44 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.63 (0.25), residues: 1094 helix: 2.18 (0.23), residues: 480 sheet: -0.09 (0.31), residues: 258 loop : -1.71 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 707 TYR 0.028 0.002 TYR A 188 PHE 0.019 0.002 PHE A 48 TRP 0.010 0.002 TRP B 629 HIS 0.005 0.001 HIS B 791 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 9324) covalent geometry : angle 0.65298 (12682) SS BOND : bond 0.00376 ( 8) SS BOND : angle 0.96234 ( 16) hydrogen bonds : bond 0.04382 ( 532) hydrogen bonds : angle 5.14438 ( 1536) link_NAG-ASN : bond 0.00380 ( 6) link_NAG-ASN : angle 2.94965 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.455 Fit side-chains REVERT: A 455 TYR cc_start: 0.8236 (t80) cc_final: 0.7880 (t80) REVERT: A 578 MET cc_start: 0.2807 (ttt) cc_final: 0.2507 (mtp) REVERT: A 580 MET cc_start: 0.5742 (mtt) cc_final: 0.5348 (mtt) REVERT: A 629 TRP cc_start: 0.3695 (m100) cc_final: 0.3137 (m100) REVERT: A 684 MET cc_start: -0.1260 (mmt) cc_final: -0.1797 (ptp) REVERT: A 725 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 727 PHE cc_start: 0.7874 (m-10) cc_final: 0.7581 (m-10) REVERT: A 731 MET cc_start: 0.8170 (mmm) cc_final: 0.7418 (ttt) REVERT: A 778 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8618 (mttm) REVERT: A 786 ASP cc_start: 0.8138 (t0) cc_final: 0.7839 (t0) REVERT: B 94 LEU cc_start: 0.7321 (mm) cc_final: 0.6978 (mm) REVERT: B 106 TRP cc_start: 0.8069 (p90) cc_final: 0.7819 (p90) REVERT: B 117 GLN cc_start: 0.7858 (pp30) cc_final: 0.7321 (pp30) REVERT: B 317 PHE cc_start: 0.7778 (m-80) cc_final: 0.7476 (m-80) REVERT: B 451 ILE cc_start: 0.8201 (mm) cc_final: 0.7988 (pt) REVERT: B 455 TYR cc_start: 0.8176 (t80) cc_final: 0.7637 (t80) REVERT: B 509 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7887 (t80) REVERT: B 517 ARG cc_start: 0.7328 (tpt170) cc_final: 0.6958 (ptm-80) REVERT: B 548 MET cc_start: 0.7750 (ptp) cc_final: 0.7427 (ptp) REVERT: B 681 MET cc_start: 0.3712 (mmp) cc_final: 0.2555 (mtp) REVERT: B 684 MET cc_start: -0.0485 (mmt) cc_final: -0.0686 (mmm) REVERT: B 727 PHE cc_start: 0.7992 (m-10) cc_final: 0.7585 (m-80) REVERT: B 731 MET cc_start: 0.7999 (mmm) cc_final: 0.7495 (ttt) REVERT: B 753 MET cc_start: 0.8720 (mmp) cc_final: 0.8032 (mmt) REVERT: B 786 ASP cc_start: 0.8121 (t0) cc_final: 0.7790 (t0) outliers start: 52 outliers final: 39 residues processed: 179 average time/residue: 0.0723 time to fit residues: 19.8031 Evaluate side-chains 171 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 765 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 476 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.214242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.157932 restraints weight = 11729.773| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 4.04 r_work: 0.3874 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9338 Z= 0.129 Angle : 0.585 8.953 12716 Z= 0.296 Chirality : 0.044 0.153 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.760 45.464 1324 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.44 % Allowed : 25.56 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.88 (0.26), residues: 1094 helix: 2.44 (0.23), residues: 478 sheet: 0.12 (0.31), residues: 250 loop : -1.67 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 127 TYR 0.017 0.001 TYR A 188 PHE 0.023 0.001 PHE B 806 TRP 0.010 0.001 TRP B 629 HIS 0.002 0.000 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9324) covalent geometry : angle 0.57552 (12682) SS BOND : bond 0.00406 ( 8) SS BOND : angle 0.97473 ( 16) hydrogen bonds : bond 0.03841 ( 532) hydrogen bonds : angle 4.71162 ( 1536) link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 2.76946 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.8019 (pmm) cc_final: 0.7714 (pmm) REVERT: A 445 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.4156 (m-10) REVERT: A 455 TYR cc_start: 0.8037 (t80) cc_final: 0.7475 (t80) REVERT: A 578 MET cc_start: 0.2704 (ttt) cc_final: 0.2412 (mtp) REVERT: A 580 MET cc_start: 0.5590 (mtt) cc_final: 0.5132 (mtt) REVERT: A 684 MET cc_start: -0.1102 (mmt) cc_final: -0.1605 (ptp) REVERT: A 727 PHE cc_start: 0.7865 (m-10) cc_final: 0.7536 (m-80) REVERT: A 731 MET cc_start: 0.8015 (mmm) cc_final: 0.7449 (ttt) REVERT: A 753 MET cc_start: 0.8697 (mmp) cc_final: 0.7970 (mmt) REVERT: B 94 LEU cc_start: 0.7434 (mm) cc_final: 0.7100 (mm) REVERT: B 106 TRP cc_start: 0.8047 (p90) cc_final: 0.7435 (p90) REVERT: B 111 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6998 (tt) REVERT: B 117 GLN cc_start: 0.7836 (pp30) cc_final: 0.7364 (pp30) REVERT: B 317 PHE cc_start: 0.7755 (m-80) cc_final: 0.7505 (m-80) REVERT: B 451 ILE cc_start: 0.8129 (mm) cc_final: 0.7890 (pt) REVERT: B 455 TYR cc_start: 0.7854 (t80) cc_final: 0.7482 (t80) REVERT: B 496 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8298 (p0) REVERT: B 509 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7734 (t80) REVERT: B 517 ARG cc_start: 0.7263 (tpt170) cc_final: 0.6918 (ptm-80) REVERT: B 548 MET cc_start: 0.7800 (ptp) cc_final: 0.7473 (ptp) REVERT: B 555 GLU cc_start: 0.8725 (tm-30) cc_final: 0.7711 (tp30) REVERT: B 727 PHE cc_start: 0.8055 (m-10) cc_final: 0.7752 (m-10) REVERT: B 731 MET cc_start: 0.8023 (mmm) cc_final: 0.7559 (ttt) REVERT: B 786 ASP cc_start: 0.8049 (t0) cc_final: 0.7674 (t0) outliers start: 44 outliers final: 33 residues processed: 171 average time/residue: 0.0713 time to fit residues: 19.1158 Evaluate side-chains 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 765 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 40.0000 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.211403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.154450 restraints weight = 11821.911| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 4.08 r_work: 0.3830 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9338 Z= 0.178 Angle : 0.621 9.656 12716 Z= 0.314 Chirality : 0.045 0.164 1462 Planarity : 0.004 0.052 1560 Dihedral : 4.805 38.284 1324 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.05 % Allowed : 25.35 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.80 (0.26), residues: 1094 helix: 2.38 (0.23), residues: 478 sheet: 0.02 (0.32), residues: 258 loop : -1.71 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 707 TYR 0.022 0.002 TYR A 188 PHE 0.031 0.002 PHE B 806 TRP 0.009 0.001 TRP A 629 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9324) covalent geometry : angle 0.61085 (12682) SS BOND : bond 0.00319 ( 8) SS BOND : angle 1.01278 ( 16) hydrogen bonds : bond 0.04012 ( 532) hydrogen bonds : angle 4.83685 ( 1536) link_NAG-ASN : bond 0.00263 ( 6) link_NAG-ASN : angle 2.93734 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7347 (mm) cc_final: 0.7067 (mm) REVERT: A 106 TRP cc_start: 0.8042 (p90) cc_final: 0.7466 (p90) REVERT: A 190 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.6656 (tp) REVERT: A 455 TYR cc_start: 0.8130 (t80) cc_final: 0.7859 (t80) REVERT: A 496 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8316 (p0) REVERT: A 578 MET cc_start: 0.2676 (ttt) cc_final: 0.2388 (mtp) REVERT: A 580 MET cc_start: 0.5643 (mtt) cc_final: 0.5259 (mtt) REVERT: A 727 PHE cc_start: 0.7858 (m-10) cc_final: 0.7534 (m-80) REVERT: A 731 MET cc_start: 0.7968 (mmm) cc_final: 0.7495 (ttt) REVERT: B 94 LEU cc_start: 0.7490 (mm) cc_final: 0.7166 (mm) REVERT: B 106 TRP cc_start: 0.8138 (p90) cc_final: 0.7473 (p90) REVERT: B 115 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 116 TYR cc_start: 0.8749 (m-80) cc_final: 0.8321 (m-80) REVERT: B 317 PHE cc_start: 0.7853 (m-80) cc_final: 0.7636 (m-80) REVERT: B 451 ILE cc_start: 0.8128 (mm) cc_final: 0.7893 (pt) REVERT: B 455 TYR cc_start: 0.7915 (t80) cc_final: 0.7596 (t80) REVERT: B 509 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7766 (t80) REVERT: B 517 ARG cc_start: 0.7262 (tpt170) cc_final: 0.6906 (ptm-80) REVERT: B 555 GLU cc_start: 0.8700 (tm-30) cc_final: 0.7673 (tp30) REVERT: B 727 PHE cc_start: 0.8011 (m-10) cc_final: 0.7710 (m-10) REVERT: B 731 MET cc_start: 0.8030 (mmm) cc_final: 0.7549 (ttt) REVERT: B 786 ASP cc_start: 0.8132 (t0) cc_final: 0.7732 (t0) outliers start: 50 outliers final: 40 residues processed: 172 average time/residue: 0.0692 time to fit residues: 18.7743 Evaluate side-chains 172 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 765 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 636 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.215050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.162277 restraints weight = 11678.525| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.77 r_work: 0.3908 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9338 Z= 0.115 Angle : 0.583 10.135 12716 Z= 0.291 Chirality : 0.044 0.207 1462 Planarity : 0.003 0.051 1560 Dihedral : 4.480 38.634 1324 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.75 % Allowed : 25.56 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.98 (0.26), residues: 1094 helix: 2.53 (0.23), residues: 478 sheet: 0.15 (0.32), residues: 250 loop : -1.62 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.015 0.001 TYR A 188 PHE 0.050 0.001 PHE A 700 TRP 0.007 0.001 TRP B 629 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9324) covalent geometry : angle 0.57358 (12682) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.78521 ( 16) hydrogen bonds : bond 0.03683 ( 532) hydrogen bonds : angle 4.45661 ( 1536) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 2.73093 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7159 (mm) cc_final: 0.6865 (mm) REVERT: A 106 TRP cc_start: 0.7959 (p90) cc_final: 0.7353 (p90) REVERT: A 190 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6564 (tp) REVERT: A 445 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.4172 (m-10) REVERT: A 455 TYR cc_start: 0.7878 (t80) cc_final: 0.7275 (t80) REVERT: A 509 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 578 MET cc_start: 0.2593 (ttt) cc_final: 0.2325 (mtp) REVERT: A 580 MET cc_start: 0.5562 (mtt) cc_final: 0.5109 (mtt) REVERT: A 727 PHE cc_start: 0.7981 (m-10) cc_final: 0.7648 (m-80) REVERT: A 731 MET cc_start: 0.8014 (mmm) cc_final: 0.7511 (ttt) REVERT: A 753 MET cc_start: 0.8694 (mmp) cc_final: 0.8038 (mmt) REVERT: B 94 LEU cc_start: 0.7252 (mm) cc_final: 0.6928 (mm) REVERT: B 106 TRP cc_start: 0.8118 (p90) cc_final: 0.7523 (p90) REVERT: B 111 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7074 (tt) REVERT: B 115 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8228 (tt) REVERT: B 117 GLN cc_start: 0.7701 (pp30) cc_final: 0.7440 (pp30) REVERT: B 451 ILE cc_start: 0.8120 (mm) cc_final: 0.7914 (pt) REVERT: B 455 TYR cc_start: 0.7756 (t80) cc_final: 0.7486 (t80) REVERT: B 509 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7698 (t80) REVERT: B 517 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6895 (ptm-80) REVERT: B 555 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7581 (tp30) REVERT: B 731 MET cc_start: 0.8019 (mmm) cc_final: 0.7587 (ttt) REVERT: B 753 MET cc_start: 0.8607 (mmp) cc_final: 0.7900 (mmt) REVERT: B 786 ASP cc_start: 0.7982 (t0) cc_final: 0.7588 (t0) outliers start: 47 outliers final: 29 residues processed: 172 average time/residue: 0.0682 time to fit residues: 18.5159 Evaluate side-chains 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 98 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.209950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.153894 restraints weight = 11817.013| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 4.04 r_work: 0.3823 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9338 Z= 0.203 Angle : 0.668 11.267 12716 Z= 0.339 Chirality : 0.047 0.188 1462 Planarity : 0.004 0.052 1560 Dihedral : 4.783 30.734 1324 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.65 % Allowed : 25.45 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.71 (0.26), residues: 1094 helix: 2.23 (0.23), residues: 480 sheet: 0.04 (0.32), residues: 258 loop : -1.70 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.023 0.002 TYR A 188 PHE 0.021 0.002 PHE B 727 TRP 0.012 0.001 TRP B 794 HIS 0.003 0.001 HIS A 791 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 9324) covalent geometry : angle 0.65825 (12682) SS BOND : bond 0.00349 ( 8) SS BOND : angle 1.01200 ( 16) hydrogen bonds : bond 0.04096 ( 532) hydrogen bonds : angle 4.84705 ( 1536) link_NAG-ASN : bond 0.00255 ( 6) link_NAG-ASN : angle 3.03327 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7486 (mm) cc_final: 0.7188 (mm) REVERT: A 152 MET cc_start: 0.7813 (pmm) cc_final: 0.7444 (pmm) REVERT: A 190 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6665 (tp) REVERT: A 455 TYR cc_start: 0.8074 (t80) cc_final: 0.7758 (t80) REVERT: A 496 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8417 (p0) REVERT: A 509 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7817 (t80) REVERT: A 578 MET cc_start: 0.2597 (ttt) cc_final: 0.2303 (mtp) REVERT: A 727 PHE cc_start: 0.7967 (m-10) cc_final: 0.7627 (m-80) REVERT: A 731 MET cc_start: 0.8017 (mmm) cc_final: 0.7496 (ttt) REVERT: A 753 MET cc_start: 0.8697 (mmp) cc_final: 0.8029 (mmt) REVERT: B 94 LEU cc_start: 0.7519 (mm) cc_final: 0.7145 (mm) REVERT: B 106 TRP cc_start: 0.8185 (p90) cc_final: 0.7542 (p90) REVERT: B 115 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7903 (tt) REVERT: B 117 GLN cc_start: 0.7720 (pp30) cc_final: 0.7438 (pp30) REVERT: B 451 ILE cc_start: 0.8110 (mm) cc_final: 0.7875 (pt) REVERT: B 455 TYR cc_start: 0.7859 (t80) cc_final: 0.7520 (t80) REVERT: B 496 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8417 (p0) REVERT: B 509 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7735 (t80) REVERT: B 517 ARG cc_start: 0.7258 (tpt170) cc_final: 0.6924 (ptm-80) REVERT: B 580 MET cc_start: 0.6761 (tmm) cc_final: 0.6499 (tmm) REVERT: B 727 PHE cc_start: 0.7914 (m-10) cc_final: 0.7629 (m-80) REVERT: B 731 MET cc_start: 0.8048 (mmm) cc_final: 0.7600 (ttt) REVERT: B 786 ASP cc_start: 0.8200 (t0) cc_final: 0.7803 (t0) outliers start: 46 outliers final: 33 residues processed: 171 average time/residue: 0.0708 time to fit residues: 18.8640 Evaluate side-chains 168 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.213408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.161518 restraints weight = 11735.589| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.52 r_work: 0.3896 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9338 Z= 0.129 Angle : 0.647 13.476 12716 Z= 0.319 Chirality : 0.045 0.223 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.395 24.137 1324 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.14 % Allowed : 26.46 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.94 (0.26), residues: 1094 helix: 2.46 (0.23), residues: 480 sheet: 0.17 (0.32), residues: 250 loop : -1.64 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 289 TYR 0.016 0.001 TYR A 188 PHE 0.020 0.001 PHE B 727 TRP 0.007 0.001 TRP B 106 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9324) covalent geometry : angle 0.63825 (12682) SS BOND : bond 0.00275 ( 8) SS BOND : angle 0.82374 ( 16) hydrogen bonds : bond 0.03781 ( 532) hydrogen bonds : angle 4.51951 ( 1536) link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 2.81440 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7158 (mm) cc_final: 0.6852 (mm) REVERT: A 106 TRP cc_start: 0.8033 (p90) cc_final: 0.7383 (p90) REVERT: A 190 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6580 (tp) REVERT: A 455 TYR cc_start: 0.7849 (t80) cc_final: 0.7441 (t80) REVERT: A 496 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8303 (p0) REVERT: A 578 MET cc_start: 0.2455 (ttt) cc_final: 0.2194 (mtp) REVERT: A 727 PHE cc_start: 0.7977 (m-10) cc_final: 0.7649 (m-80) REVERT: A 731 MET cc_start: 0.8023 (mmm) cc_final: 0.7557 (ttt) REVERT: A 753 MET cc_start: 0.8654 (mmp) cc_final: 0.7950 (mmt) REVERT: B 94 LEU cc_start: 0.7274 (mm) cc_final: 0.6945 (mm) REVERT: B 106 TRP cc_start: 0.8134 (p90) cc_final: 0.7634 (p90) REVERT: B 111 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7103 (tt) REVERT: B 115 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7973 (tt) REVERT: B 117 GLN cc_start: 0.7693 (pp30) cc_final: 0.7425 (pp30) REVERT: B 455 TYR cc_start: 0.7744 (t80) cc_final: 0.7506 (t80) REVERT: B 509 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7696 (t80) REVERT: B 517 ARG cc_start: 0.7263 (tpt170) cc_final: 0.6924 (ptm-80) REVERT: B 555 GLU cc_start: 0.8709 (tm-30) cc_final: 0.7681 (tp30) REVERT: B 580 MET cc_start: 0.6806 (tmm) cc_final: 0.6516 (tmm) REVERT: B 731 MET cc_start: 0.8042 (mmm) cc_final: 0.7647 (ttt) REVERT: B 753 MET cc_start: 0.8640 (mmp) cc_final: 0.8035 (mmt) REVERT: B 786 ASP cc_start: 0.8021 (t0) cc_final: 0.7625 (t0) outliers start: 41 outliers final: 31 residues processed: 166 average time/residue: 0.0677 time to fit residues: 17.7171 Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.209015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.153732 restraints weight = 11648.999| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.84 r_work: 0.3816 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9338 Z= 0.221 Angle : 0.708 10.645 12716 Z= 0.357 Chirality : 0.049 0.350 1462 Planarity : 0.005 0.052 1560 Dihedral : 4.826 23.637 1324 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.55 % Allowed : 26.57 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.70 (0.26), residues: 1094 helix: 2.18 (0.23), residues: 480 sheet: 0.10 (0.32), residues: 254 loop : -1.69 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.025 0.002 TYR A 188 PHE 0.015 0.002 PHE A 761 TRP 0.012 0.002 TRP B 794 HIS 0.010 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 9324) covalent geometry : angle 0.69799 (12682) SS BOND : bond 0.00365 ( 8) SS BOND : angle 1.02277 ( 16) hydrogen bonds : bond 0.04195 ( 532) hydrogen bonds : angle 4.92862 ( 1536) link_NAG-ASN : bond 0.00294 ( 6) link_NAG-ASN : angle 3.13478 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2363.12 seconds wall clock time: 41 minutes 16.47 seconds (2476.47 seconds total)