Starting phenix.real_space_refine on Wed Apr 30 01:17:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k13_36785/04_2025/8k13_36785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k13_36785/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k13_36785/04_2025/8k13_36785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k13_36785/04_2025/8k13_36785.map" model { file = "/net/cci-nas-00/data/ceres_data/8k13_36785/04_2025/8k13_36785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k13_36785/04_2025/8k13_36785.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG: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: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG: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: 5.66, per 1000 atoms: 0.62 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 1.08 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: 2.80 Time building geometry restraints manager: 2.83 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: 0.04 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (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 TRP 0.005 0.001 TRP A 695 HIS 0.005 0.001 HIS B 229 PHE 0.014 0.001 PHE A 727 TYR 0.013 0.001 TYR B 269 ARG 0.002 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 6) link_NAG-ASN : angle 2.63909 ( 18) hydrogen bonds : bond 0.16691 ( 532) hydrogen bonds : angle 6.76235 ( 1536) SS BOND : bond 0.00188 ( 8) SS BOND : angle 1.25263 ( 16) covalent geometry : bond 0.00328 ( 9324) covalent geometry : angle 0.58443 (12682) *********************** 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 : 0.928 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: 0.7406 (t80) REVERT: A 681 MET cc_start: 0.3968 (mmp) cc_final: 0.2306 (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: 0.7595 (m-10) REVERT: B 455 TYR cc_start: 0.7983 (t80) cc_final: 0.7347 (t80) REVERT: B 485 CYS cc_start: 0.6209 (t) cc_final: 0.5686 (t) REVERT: B 575 THR cc_start: 0.8078 (p) cc_final: 0.7801 (t) REVERT: B 681 MET cc_start: 0.3850 (mmp) cc_final: 0.2282 (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: 0.1856 time to fit residues: 56.1398 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 : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 = 0.4590 r_free = 0.4590 target = 0.213323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157020 restraints weight = 11602.199| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 4.02 r_work: 0.3829 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 9338 Z= 0.209 Angle : 0.648 8.281 12716 Z= 0.336 Chirality : 0.046 0.146 1462 Planarity : 0.005 0.050 1560 Dihedral : 6.311 55.969 1324 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.35 % Allowed : 23.64 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1094 helix: 2.21 (0.23), residues: 482 sheet: 0.32 (0.33), residues: 248 loop : -1.64 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 629 HIS 0.003 0.001 HIS A 791 PHE 0.015 0.002 PHE B 796 TYR 0.026 0.002 TYR A 188 ARG 0.003 0.001 ARG A 776 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 6) link_NAG-ASN : angle 2.73297 ( 18) hydrogen bonds : bond 0.04482 ( 532) hydrogen bonds : angle 5.22096 ( 1536) SS BOND : bond 0.00465 ( 8) SS BOND : angle 1.39466 ( 16) covalent geometry : bond 0.00502 ( 9324) covalent geometry : angle 0.63915 (12682) *********************** 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 197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7900 (t0) REVERT: A 316 ILE cc_start: 0.8440 (pp) cc_final: 0.8202 (pp) REVERT: A 455 TYR cc_start: 0.8045 (t80) cc_final: 0.7657 (t80) REVERT: A 580 MET cc_start: 0.5871 (mtt) cc_final: 0.5445 (mtt) REVERT: A 681 MET cc_start: 0.3523 (mmp) cc_final: 0.1677 (ttm) REVERT: A 684 MET cc_start: -0.0622 (mmt) cc_final: -0.1109 (pmm) REVERT: B 106 TRP cc_start: 0.8031 (p90) cc_final: 0.7597 (p90) REVERT: B 117 GLN cc_start: 0.7705 (pp30) cc_final: 0.7276 (pp30) REVERT: B 325 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6847 (pp) REVERT: B 455 TYR cc_start: 0.8160 (t80) cc_final: 0.7933 (t80) REVERT: B 555 GLU cc_start: 0.8809 (tm-30) cc_final: 0.7912 (tp30) REVERT: B 681 MET cc_start: 0.3154 (mmp) cc_final: 0.2129 (ttm) REVERT: B 727 PHE cc_start: 0.7840 (m-10) cc_final: 0.7373 (m-10) REVERT: B 731 MET cc_start: 0.7883 (mmm) cc_final: 0.7178 (ttt) REVERT: B 753 MET cc_start: 0.7996 (mmt) cc_final: 0.7587 (mmt) REVERT: B 769 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: B 778 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8723 (mttm) outliers start: 53 outliers final: 26 residues processed: 185 average time/residue: 0.1634 time to fit residues: 45.4398 Evaluate side-chains 162 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 484 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 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.216742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.163263 restraints weight = 11736.305| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.76 r_work: 0.3890 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9338 Z= 0.136 Angle : 0.574 10.279 12716 Z= 0.294 Chirality : 0.044 0.146 1462 Planarity : 0.004 0.046 1560 Dihedral : 5.958 58.288 1324 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.04 % Allowed : 23.74 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1094 helix: 2.42 (0.23), residues: 480 sheet: 0.42 (0.33), residues: 240 loop : -1.64 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 629 HIS 0.007 0.001 HIS B 229 PHE 0.022 0.001 PHE B 700 TYR 0.017 0.001 TYR A 188 ARG 0.003 0.000 ARG A 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 2.57473 ( 18) hydrogen bonds : bond 0.04070 ( 532) hydrogen bonds : angle 4.84898 ( 1536) SS BOND : bond 0.00281 ( 8) SS BOND : angle 0.92050 ( 16) covalent geometry : bond 0.00316 ( 9324) covalent geometry : angle 0.56546 (12682) *********************** 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 191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7627 (pt) cc_final: 0.7417 (pp) REVERT: A 455 TYR cc_start: 0.8155 (t80) cc_final: 0.7354 (t80) REVERT: A 580 MET cc_start: 0.5782 (mtt) cc_final: 0.5305 (mtt) REVERT: A 681 MET cc_start: 0.3545 (mmp) cc_final: 0.2239 (ttm) REVERT: A 684 MET cc_start: -0.0627 (mmt) cc_final: -0.1190 (ptp) REVERT: A 727 PHE cc_start: 0.7819 (m-10) cc_final: 0.7471 (m-10) REVERT: A 731 MET cc_start: 0.8170 (mmm) cc_final: 0.7267 (ttt) REVERT: B 111 LEU cc_start: 0.7378 (mp) cc_final: 0.7039 (tt) REVERT: B 117 GLN cc_start: 0.7707 (pp30) cc_final: 0.7239 (pp30) REVERT: B 325 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6866 (pp) REVERT: B 451 ILE cc_start: 0.8219 (mm) cc_final: 0.7980 (pt) REVERT: B 455 TYR cc_start: 0.8153 (t80) cc_final: 0.7789 (t80) REVERT: B 517 ARG cc_start: 0.7399 (tpt170) cc_final: 0.7076 (ptm-80) REVERT: B 545 PHE cc_start: 0.7561 (m-10) cc_final: 0.7334 (m-10) REVERT: B 555 GLU cc_start: 0.8759 (tm-30) cc_final: 0.7950 (tp30) REVERT: B 580 MET cc_start: 0.5380 (mtt) cc_final: 0.5083 (mtt) REVERT: B 681 MET cc_start: 0.3368 (mmp) cc_final: 0.1938 (mtp) REVERT: B 684 MET cc_start: 0.0220 (mmm) cc_final: -0.0354 (ptp) REVERT: B 727 PHE cc_start: 0.7808 (m-10) cc_final: 0.7364 (m-10) REVERT: B 731 MET cc_start: 0.8193 (mmm) cc_final: 0.7306 (ttt) REVERT: B 753 MET cc_start: 0.8285 (mmt) cc_final: 0.7754 (mmt) outliers start: 40 outliers final: 23 residues processed: 183 average time/residue: 0.1572 time to fit residues: 43.6817 Evaluate side-chains 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 VAL 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 A residue 771 THR 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 163 VAL 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 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 714 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4563 r_free = 0.4563 target = 0.209959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.153845 restraints weight = 11682.812| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 4.05 r_work: 0.3812 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 9338 Z= 0.228 Angle : 0.649 7.630 12716 Z= 0.335 Chirality : 0.047 0.152 1462 Planarity : 0.005 0.050 1560 Dihedral : 5.539 52.128 1324 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.25 % Allowed : 23.84 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1094 helix: 2.17 (0.23), residues: 480 sheet: -0.10 (0.31), residues: 258 loop : -1.69 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 629 HIS 0.009 0.001 HIS B 50 PHE 0.021 0.002 PHE B 806 TYR 0.025 0.002 TYR A 188 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 6) link_NAG-ASN : angle 2.84541 ( 18) hydrogen bonds : bond 0.04363 ( 532) hydrogen bonds : angle 5.09139 ( 1536) SS BOND : bond 0.00389 ( 8) SS BOND : angle 1.00792 ( 16) covalent geometry : bond 0.00550 ( 9324) covalent geometry : angle 0.64017 (12682) *********************** 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 190 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.953 Fit side-chains REVERT: A 106 TRP cc_start: 0.8109 (p90) cc_final: 0.7578 (p90) REVERT: A 445 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.3884 (m-10) REVERT: A 455 TYR cc_start: 0.8263 (t80) cc_final: 0.7924 (t80) REVERT: A 580 MET cc_start: 0.5823 (mtt) cc_final: 0.5426 (mtt) REVERT: A 684 MET cc_start: -0.1290 (mmt) cc_final: -0.1797 (ptp) REVERT: A 723 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 727 PHE cc_start: 0.7919 (m-10) cc_final: 0.7542 (m-80) REVERT: A 731 MET cc_start: 0.8163 (mmm) cc_final: 0.7353 (ttt) REVERT: A 759 TYR cc_start: 0.8047 (t80) cc_final: 0.7790 (t80) REVERT: A 778 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8591 (mttm) REVERT: A 786 ASP cc_start: 0.8036 (t0) cc_final: 0.7775 (t0) REVERT: B 106 TRP cc_start: 0.8087 (p90) cc_final: 0.7552 (p90) REVERT: B 117 GLN cc_start: 0.7923 (pp30) cc_final: 0.7438 (pp30) REVERT: B 451 ILE cc_start: 0.8170 (mm) cc_final: 0.7955 (pt) REVERT: B 455 TYR cc_start: 0.8243 (t80) cc_final: 0.7718 (t80) REVERT: B 509 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7922 (t80) REVERT: B 681 MET cc_start: 0.3703 (mmp) cc_final: 0.2551 (mtp) REVERT: B 727 PHE cc_start: 0.7993 (m-10) cc_final: 0.7584 (m-80) REVERT: B 731 MET cc_start: 0.8249 (mmm) cc_final: 0.7443 (ttt) REVERT: B 786 ASP cc_start: 0.8164 (t0) cc_final: 0.7921 (t0) outliers start: 52 outliers final: 35 residues processed: 181 average time/residue: 0.1546 time to fit residues: 42.6583 Evaluate side-chains 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 236 VAL 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 723 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 65 SER 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 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 Chi-restraints excluded: chain B residue 765 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 A 476 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.215194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.159934 restraints weight = 11645.425| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 4.08 r_work: 0.3880 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9338 Z= 0.124 Angle : 0.577 8.338 12716 Z= 0.293 Chirality : 0.044 0.151 1462 Planarity : 0.004 0.049 1560 Dihedral : 4.885 50.413 1324 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.74 % Allowed : 25.86 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1094 helix: 2.41 (0.23), residues: 478 sheet: 0.10 (0.31), residues: 254 loop : -1.66 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.002 0.000 HIS B 178 PHE 0.035 0.001 PHE B 806 TYR 0.016 0.001 TYR A 188 ARG 0.001 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 2.66658 ( 18) hydrogen bonds : bond 0.03840 ( 532) hydrogen bonds : angle 4.66640 ( 1536) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.82326 ( 16) covalent geometry : bond 0.00284 ( 9324) covalent geometry : angle 0.56844 (12682) *********************** 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 181 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.8043 (p90) cc_final: 0.7699 (p90) REVERT: A 445 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.4006 (m-10) REVERT: A 455 TYR cc_start: 0.8017 (t80) cc_final: 0.7763 (t80) REVERT: A 580 MET cc_start: 0.5644 (mtt) cc_final: 0.5171 (mtt) REVERT: A 684 MET cc_start: -0.1304 (mmt) cc_final: -0.1777 (ptp) REVERT: A 723 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 727 PHE cc_start: 0.8011 (m-10) cc_final: 0.7645 (m-80) REVERT: A 731 MET cc_start: 0.8119 (mmm) cc_final: 0.7367 (ttt) REVERT: A 753 MET cc_start: 0.8706 (mmp) cc_final: 0.7966 (mmt) REVERT: A 778 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8557 (mttm) REVERT: B 94 LEU cc_start: 0.7063 (mm) cc_final: 0.6590 (mm) REVERT: B 106 TRP cc_start: 0.8036 (p90) cc_final: 0.7732 (p90) REVERT: B 111 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7022 (tt) REVERT: B 117 GLN cc_start: 0.7821 (pp30) cc_final: 0.7343 (pp30) REVERT: B 317 PHE cc_start: 0.7813 (m-80) cc_final: 0.7517 (m-80) REVERT: B 451 ILE cc_start: 0.8205 (mm) cc_final: 0.7975 (pt) REVERT: B 455 TYR cc_start: 0.7810 (t80) cc_final: 0.7592 (t80) REVERT: B 496 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8249 (p0) REVERT: B 509 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7781 (t80) REVERT: B 517 ARG cc_start: 0.7308 (tpt170) cc_final: 0.6916 (ptm-80) REVERT: B 555 GLU cc_start: 0.8733 (tm-30) cc_final: 0.7714 (tp30) REVERT: B 681 MET cc_start: 0.3558 (mmp) cc_final: 0.2466 (mtp) REVERT: B 727 PHE cc_start: 0.8010 (m-10) cc_final: 0.7589 (m-80) REVERT: B 731 MET cc_start: 0.8022 (mmm) cc_final: 0.7435 (ttt) REVERT: B 753 MET cc_start: 0.8732 (mmp) cc_final: 0.8014 (mmt) REVERT: B 786 ASP cc_start: 0.8042 (t0) cc_final: 0.7745 (t0) outliers start: 37 outliers final: 23 residues processed: 173 average time/residue: 0.1598 time to fit residues: 41.9746 Evaluate side-chains 166 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 238 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 484 LEU 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 723 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 166 LEU Chi-restraints excluded: chain B residue 173 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 98 optimal weight: 50.0000 chunk 60 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 50 HIS ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.215078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.160063 restraints weight = 11585.726| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.97 r_work: 0.3885 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9338 Z= 0.123 Angle : 0.562 9.023 12716 Z= 0.285 Chirality : 0.044 0.155 1462 Planarity : 0.003 0.050 1560 Dihedral : 4.753 46.601 1324 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.95 % Allowed : 25.76 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1094 helix: 2.45 (0.23), residues: 480 sheet: 0.12 (0.31), residues: 254 loop : -1.59 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.002 0.000 HIS A 168 PHE 0.023 0.001 PHE A 806 TYR 0.015 0.001 TYR B 188 ARG 0.002 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 6) link_NAG-ASN : angle 2.63782 ( 18) hydrogen bonds : bond 0.03729 ( 532) hydrogen bonds : angle 4.55420 ( 1536) SS BOND : bond 0.00260 ( 8) SS BOND : angle 0.92350 ( 16) covalent geometry : bond 0.00286 ( 9324) covalent geometry : angle 0.55293 (12682) *********************** 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 189 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.8091 (p90) cc_final: 0.7771 (p90) REVERT: A 445 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.4128 (m-10) REVERT: A 455 TYR cc_start: 0.7922 (t80) cc_final: 0.7139 (t80) REVERT: A 457 LEU cc_start: 0.8910 (mm) cc_final: 0.8699 (mm) REVERT: A 496 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8276 (p0) REVERT: A 548 MET cc_start: 0.7193 (ptp) cc_final: 0.6866 (mmt) REVERT: A 580 MET cc_start: 0.5675 (mtt) cc_final: 0.5210 (mtt) REVERT: A 684 MET cc_start: -0.1109 (mmt) cc_final: -0.1583 (ptp) REVERT: A 723 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 727 PHE cc_start: 0.7993 (m-10) cc_final: 0.7631 (m-80) REVERT: A 731 MET cc_start: 0.8007 (mmm) cc_final: 0.7434 (ttt) REVERT: A 778 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8538 (mttm) REVERT: A 783 ILE cc_start: 0.8294 (tt) cc_final: 0.7924 (tp) REVERT: B 94 LEU cc_start: 0.7159 (mm) cc_final: 0.6803 (mm) REVERT: B 106 TRP cc_start: 0.8110 (p90) cc_final: 0.7831 (p90) REVERT: B 111 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7095 (tt) REVERT: B 117 GLN cc_start: 0.7822 (pp30) cc_final: 0.7382 (pp30) REVERT: B 317 PHE cc_start: 0.7814 (m-80) cc_final: 0.7591 (m-80) REVERT: B 445 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.3899 (m-80) REVERT: B 451 ILE cc_start: 0.8100 (mm) cc_final: 0.7877 (pt) REVERT: B 455 TYR cc_start: 0.8043 (t80) cc_final: 0.7612 (t80) REVERT: B 496 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8235 (p0) REVERT: B 509 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 517 ARG cc_start: 0.7305 (tpt170) cc_final: 0.6903 (ptm-80) REVERT: B 555 GLU cc_start: 0.8604 (tm-30) cc_final: 0.7545 (tp30) REVERT: B 580 MET cc_start: 0.5588 (mtt) cc_final: 0.5190 (mtt) REVERT: B 681 MET cc_start: 0.3639 (mmp) cc_final: 0.2432 (mtp) REVERT: B 727 PHE cc_start: 0.8065 (m-10) cc_final: 0.7757 (m-10) REVERT: B 731 MET cc_start: 0.8081 (mmm) cc_final: 0.7552 (ttt) outliers start: 49 outliers final: 33 residues processed: 177 average time/residue: 0.1544 time to fit residues: 41.4242 Evaluate side-chains 177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 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 723 LEU Chi-restraints excluded: chain A residue 758 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 144 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 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 Chi-restraints excluded: chain B residue 783 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 58 optimal weight: 8.9990 chunk 16 optimal weight: 0.0670 overall best weight: 1.4522 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.213561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.158077 restraints weight = 11720.685| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 4.24 r_work: 0.3860 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9338 Z= 0.144 Angle : 0.595 12.625 12716 Z= 0.298 Chirality : 0.044 0.188 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.637 39.497 1324 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.35 % Allowed : 25.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1094 helix: 2.47 (0.23), residues: 480 sheet: 0.11 (0.32), residues: 258 loop : -1.59 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.002 0.001 HIS B 791 PHE 0.035 0.001 PHE A 806 TYR 0.018 0.001 TYR B 188 ARG 0.001 0.000 ARG B 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 6) link_NAG-ASN : angle 2.74336 ( 18) hydrogen bonds : bond 0.03799 ( 532) hydrogen bonds : angle 4.55709 ( 1536) SS BOND : bond 0.00277 ( 8) SS BOND : angle 0.83724 ( 16) covalent geometry : bond 0.00341 ( 9324) covalent geometry : angle 0.58620 (12682) *********************** 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 191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.8091 (p90) cc_final: 0.7811 (p90) REVERT: A 152 MET cc_start: 0.8082 (pmm) cc_final: 0.7755 (pmm) REVERT: A 445 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.4164 (m-10) REVERT: A 455 TYR cc_start: 0.7970 (t80) cc_final: 0.7196 (t80) REVERT: A 457 LEU cc_start: 0.8944 (mm) cc_final: 0.8642 (mm) REVERT: A 496 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8273 (p0) REVERT: A 548 MET cc_start: 0.7388 (ptp) cc_final: 0.7133 (mmt) REVERT: A 580 MET cc_start: 0.5693 (mtt) cc_final: 0.5216 (mtt) REVERT: A 684 MET cc_start: -0.1145 (mmt) cc_final: -0.1650 (ptp) REVERT: A 723 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8550 (mp) REVERT: A 727 PHE cc_start: 0.8031 (m-10) cc_final: 0.7686 (m-80) REVERT: A 731 MET cc_start: 0.8049 (mmm) cc_final: 0.7486 (ttt) REVERT: A 753 MET cc_start: 0.8648 (mmp) cc_final: 0.8057 (mmt) REVERT: A 778 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8562 (mttm) REVERT: B 94 LEU cc_start: 0.7217 (mm) cc_final: 0.6797 (mm) REVERT: B 106 TRP cc_start: 0.8108 (p90) cc_final: 0.7835 (p90) REVERT: B 111 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7069 (tt) REVERT: B 115 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8136 (tt) REVERT: B 117 GLN cc_start: 0.7858 (pp30) cc_final: 0.7427 (pp30) REVERT: B 451 ILE cc_start: 0.8094 (mm) cc_final: 0.7884 (pt) REVERT: B 455 TYR cc_start: 0.7929 (t80) cc_final: 0.7449 (t80) REVERT: B 509 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7740 (t80) REVERT: B 517 ARG cc_start: 0.7252 (tpt170) cc_final: 0.6861 (ptm-80) REVERT: B 555 GLU cc_start: 0.8600 (tm-30) cc_final: 0.7509 (tp30) REVERT: B 727 PHE cc_start: 0.8033 (m-10) cc_final: 0.7733 (m-10) REVERT: B 731 MET cc_start: 0.8043 (mmm) cc_final: 0.7565 (ttt) REVERT: B 753 MET cc_start: 0.8733 (mmp) cc_final: 0.8134 (mmt) outliers start: 53 outliers final: 36 residues processed: 179 average time/residue: 0.1591 time to fit residues: 43.1500 Evaluate side-chains 179 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 721 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 758 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 115 LEU Chi-restraints excluded: chain B residue 144 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 783 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.213937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.158918 restraints weight = 11948.266| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 4.22 r_work: 0.3870 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9338 Z= 0.144 Angle : 0.616 12.974 12716 Z= 0.307 Chirality : 0.045 0.200 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.538 33.921 1324 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.15 % Allowed : 25.66 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1094 helix: 2.46 (0.23), residues: 482 sheet: 0.11 (0.32), residues: 258 loop : -1.58 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 629 HIS 0.003 0.001 HIS A 541 PHE 0.051 0.001 PHE A 700 TYR 0.017 0.001 TYR B 188 ARG 0.001 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 6) link_NAG-ASN : angle 2.73683 ( 18) hydrogen bonds : bond 0.03842 ( 532) hydrogen bonds : angle 4.56658 ( 1536) SS BOND : bond 0.00279 ( 8) SS BOND : angle 0.80592 ( 16) covalent geometry : bond 0.00343 ( 9324) covalent geometry : angle 0.60737 (12682) *********************** 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 186 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7861 (pmm) cc_final: 0.7517 (pmm) REVERT: A 190 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6597 (tp) REVERT: A 445 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.4186 (m-10) REVERT: A 455 TYR cc_start: 0.7844 (t80) cc_final: 0.7400 (t80) REVERT: A 457 LEU cc_start: 0.8993 (mm) cc_final: 0.8660 (mm) REVERT: A 496 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8283 (p0) REVERT: A 580 MET cc_start: 0.5666 (mtt) cc_final: 0.5203 (mtt) REVERT: A 629 TRP cc_start: 0.4119 (m100) cc_final: 0.3784 (m-10) REVERT: A 723 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8526 (mp) REVERT: A 727 PHE cc_start: 0.8030 (m-10) cc_final: 0.7685 (m-80) REVERT: A 731 MET cc_start: 0.8038 (mmm) cc_final: 0.7501 (ttt) REVERT: A 753 MET cc_start: 0.8686 (mmp) cc_final: 0.7948 (mmt) REVERT: A 778 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8554 (mttm) REVERT: B 94 LEU cc_start: 0.7207 (mm) cc_final: 0.6820 (mm) REVERT: B 106 TRP cc_start: 0.8091 (p90) cc_final: 0.7798 (p90) REVERT: B 111 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7052 (tt) REVERT: B 115 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 117 GLN cc_start: 0.7804 (pp30) cc_final: 0.7401 (pp30) REVERT: B 451 ILE cc_start: 0.8117 (mm) cc_final: 0.7893 (pt) REVERT: B 455 TYR cc_start: 0.7803 (t80) cc_final: 0.7520 (t80) REVERT: B 496 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8272 (p0) REVERT: B 509 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7685 (t80) REVERT: B 517 ARG cc_start: 0.7256 (tpt170) cc_final: 0.6856 (ptm-80) REVERT: B 555 GLU cc_start: 0.8588 (tm-30) cc_final: 0.7498 (tp30) REVERT: B 727 PHE cc_start: 0.8093 (m-10) cc_final: 0.7866 (m-10) REVERT: B 731 MET cc_start: 0.8042 (mmm) cc_final: 0.7577 (ttt) outliers start: 51 outliers final: 35 residues processed: 172 average time/residue: 0.1559 time to fit residues: 40.9686 Evaluate side-chains 177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 723 LEU Chi-restraints excluded: chain A residue 758 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 115 LEU Chi-restraints excluded: chain B residue 144 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 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 636 HIS Chi-restraints excluded: chain B residue 714 LEU 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 65 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4610 r_free = 0.4610 target = 0.215722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.161016 restraints weight = 11645.169| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 4.34 r_work: 0.3892 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9338 Z= 0.118 Angle : 0.591 11.705 12716 Z= 0.293 Chirality : 0.044 0.192 1462 Planarity : 0.003 0.049 1560 Dihedral : 4.317 30.885 1324 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.65 % Allowed : 25.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1094 helix: 2.59 (0.23), residues: 482 sheet: 0.15 (0.32), residues: 254 loop : -1.53 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 106 HIS 0.006 0.001 HIS B 636 PHE 0.051 0.001 PHE A 700 TYR 0.014 0.001 TYR B 188 ARG 0.001 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 6) link_NAG-ASN : angle 2.64671 ( 18) hydrogen bonds : bond 0.03625 ( 532) hydrogen bonds : angle 4.41229 ( 1536) SS BOND : bond 0.00245 ( 8) SS BOND : angle 0.72426 ( 16) covalent geometry : bond 0.00271 ( 9324) covalent geometry : angle 0.58271 (12682) *********************** 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 179 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7809 (pmm) cc_final: 0.7521 (pmm) REVERT: A 190 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6563 (tp) REVERT: A 445 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.4318 (m-10) REVERT: A 455 TYR cc_start: 0.7814 (t80) cc_final: 0.7258 (t80) REVERT: A 457 LEU cc_start: 0.9013 (mm) cc_final: 0.8661 (mm) REVERT: A 496 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8263 (p0) REVERT: A 580 MET cc_start: 0.5633 (mtt) cc_final: 0.5141 (mtt) REVERT: A 723 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 727 PHE cc_start: 0.8052 (m-10) cc_final: 0.7824 (m-80) REVERT: A 731 MET cc_start: 0.8046 (mmm) cc_final: 0.7528 (ttt) REVERT: B 94 LEU cc_start: 0.7187 (mm) cc_final: 0.6881 (mm) REVERT: B 111 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7059 (tt) REVERT: B 117 GLN cc_start: 0.7823 (pp30) cc_final: 0.7417 (pp30) REVERT: B 445 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.4125 (m-10) REVERT: B 451 ILE cc_start: 0.8098 (mm) cc_final: 0.7896 (pt) REVERT: B 455 TYR cc_start: 0.7725 (t80) cc_final: 0.7435 (t80) REVERT: B 496 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8255 (p0) REVERT: B 509 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7705 (t80) REVERT: B 517 ARG cc_start: 0.7264 (tpt170) cc_final: 0.6908 (ptm-80) REVERT: B 555 GLU cc_start: 0.8667 (tm-30) cc_final: 0.7672 (tp30) REVERT: B 731 MET cc_start: 0.8041 (mmm) cc_final: 0.7618 (ttt) REVERT: B 753 MET cc_start: 0.8696 (mmp) cc_final: 0.8017 (mmt) outliers start: 46 outliers final: 31 residues processed: 168 average time/residue: 0.1493 time to fit residues: 38.5179 Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 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 584 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 723 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 144 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 PHE 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 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 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4589 r_free = 0.4589 target = 0.213886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.161065 restraints weight = 11804.461| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.89 r_work: 0.3885 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9338 Z= 0.137 Angle : 0.629 13.991 12716 Z= 0.308 Chirality : 0.045 0.221 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.407 30.991 1324 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.55 % Allowed : 26.26 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1094 helix: 2.55 (0.23), residues: 482 sheet: 0.18 (0.32), residues: 254 loop : -1.54 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 106 HIS 0.003 0.001 HIS B 168 PHE 0.051 0.002 PHE A 700 TYR 0.016 0.001 TYR B 188 ARG 0.001 0.000 ARG A 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 2.69826 ( 18) hydrogen bonds : bond 0.03745 ( 532) hydrogen bonds : angle 4.47833 ( 1536) SS BOND : bond 0.00265 ( 8) SS BOND : angle 0.79814 ( 16) covalent geometry : bond 0.00328 ( 9324) covalent geometry : angle 0.62105 (12682) ********************** 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 182 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7307 (mm) cc_final: 0.7004 (mm) REVERT: A 152 MET cc_start: 0.7850 (pmm) cc_final: 0.7567 (pmm) REVERT: A 190 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6557 (tp) REVERT: A 445 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.4290 (m-10) REVERT: A 455 TYR cc_start: 0.7837 (t80) cc_final: 0.7285 (t80) REVERT: A 496 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8309 (p0) REVERT: A 723 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 727 PHE cc_start: 0.8072 (m-10) cc_final: 0.7844 (m-80) REVERT: A 731 MET cc_start: 0.8039 (mmm) cc_final: 0.7526 (ttt) REVERT: B 94 LEU cc_start: 0.7318 (mm) cc_final: 0.6977 (mm) REVERT: B 111 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7050 (tt) REVERT: B 117 GLN cc_start: 0.7792 (pp30) cc_final: 0.7370 (pp30) REVERT: B 451 ILE cc_start: 0.8100 (mm) cc_final: 0.7889 (pt) REVERT: B 455 TYR cc_start: 0.7710 (t80) cc_final: 0.7375 (t80) REVERT: B 496 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8295 (p0) REVERT: B 509 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7688 (t80) REVERT: B 517 ARG cc_start: 0.7262 (tpt170) cc_final: 0.6903 (ptm-80) REVERT: B 555 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7541 (tp30) REVERT: B 731 MET cc_start: 0.8043 (mmm) cc_final: 0.7625 (ttt) REVERT: B 753 MET cc_start: 0.8714 (mmp) cc_final: 0.8026 (mmt) outliers start: 45 outliers final: 32 residues processed: 170 average time/residue: 0.1881 time to fit residues: 49.6733 Evaluate side-chains 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 584 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 723 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 144 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 PHE 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 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 83 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS B 636 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.216090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.164418 restraints weight = 11758.122| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.78 r_work: 0.3923 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3965 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= 0.118 Angle : 0.614 12.475 12716 Z= 0.301 Chirality : 0.045 0.304 1462 Planarity : 0.003 0.049 1560 Dihedral : 4.233 27.651 1324 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.44 % Allowed : 26.26 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1094 helix: 2.64 (0.23), residues: 482 sheet: 0.28 (0.32), residues: 248 loop : -1.49 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 106 HIS 0.002 0.000 HIS B 168 PHE 0.051 0.001 PHE A 700 TYR 0.014 0.001 TYR B 188 ARG 0.001 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 2.63742 ( 18) hydrogen bonds : bond 0.03609 ( 532) hydrogen bonds : angle 4.36383 ( 1536) SS BOND : bond 0.00247 ( 8) SS BOND : angle 0.74929 ( 16) covalent geometry : bond 0.00274 ( 9324) covalent geometry : angle 0.60637 (12682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4630.43 seconds wall clock time: 80 minutes 30.38 seconds (4830.38 seconds total)