Starting phenix.real_space_refine on Sat Dec 28 20:20:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k13_36785/12_2024/8k13_36785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k13_36785/12_2024/8k13_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_36785/12_2024/8k13_36785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k13_36785/12_2024/8k13_36785.map" model { file = "/net/cci-nas-00/data/ceres_data/8k13_36785/12_2024/8k13_36785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k13_36785/12_2024/8k13_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.71, per 1000 atoms: 0.63 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: 2.70 Conformation dependent library (CDL) restraints added in 1.0 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: 1.14 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: 3.31 Time building geometry restraints manager: 3.02 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: 0.00 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: 0.220 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- 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 9324 Z= 0.206 Angle : 0.584 7.712 12682 Z= 0.328 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 *********************** 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 : 1.102 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: 0.1968 time to fit residues: 59.3377 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 : 1.237 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 9324 Z= 0.320 Angle : 0.639 8.281 12682 Z= 0.334 Chirality : 0.046 0.146 1462 Planarity : 0.005 0.050 1560 Dihedral : 6.311 55.970 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 *********************** 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 : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ILE cc_start: 0.8247 (pp) cc_final: 0.7965 (pp) REVERT: A 455 TYR cc_start: 0.7850 (t80) cc_final: 0.7584 (t80) REVERT: A 580 MET cc_start: 0.5805 (mtt) cc_final: 0.5585 (mtt) REVERT: A 681 MET cc_start: 0.4129 (mmp) cc_final: 0.2272 (ttm) REVERT: A 684 MET cc_start: -0.0241 (mmt) cc_final: -0.1141 (pmm) REVERT: B 106 TRP cc_start: 0.7360 (p90) cc_final: 0.7095 (p90) REVERT: B 681 MET cc_start: 0.3824 (mmp) cc_final: 0.2879 (ttm) REVERT: B 769 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7225 (pm20) outliers start: 53 outliers final: 26 residues processed: 185 average time/residue: 0.1731 time to fit residues: 48.1289 Evaluate side-chains 160 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 9324 Z= 0.326 Angle : 0.640 9.977 12682 Z= 0.331 Chirality : 0.046 0.149 1462 Planarity : 0.005 0.052 1560 Dihedral : 5.820 52.041 1324 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.35 % Allowed : 23.13 % Favored : 71.52 % 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: 0.68 (0.26), residues: 1094 helix: 2.17 (0.23), residues: 480 sheet: 0.20 (0.32), residues: 240 loop : -1.73 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 629 HIS 0.006 0.001 HIS A 229 PHE 0.022 0.002 PHE B 700 TYR 0.023 0.002 TYR A 188 ARG 0.002 0.000 ARG A 127 *********************** 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 189 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 681 MET cc_start: 0.4382 (mmp) cc_final: 0.3262 (ttm) REVERT: A 684 MET cc_start: -0.0194 (mmt) cc_final: -0.1316 (ptp) REVERT: A 759 TYR cc_start: 0.7575 (t80) cc_final: 0.7292 (t80) REVERT: B 509 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7768 (t80) REVERT: B 580 MET cc_start: 0.5677 (mtt) cc_final: 0.5452 (mtt) REVERT: B 681 MET cc_start: 0.4157 (mmp) cc_final: 0.3126 (ttm) REVERT: B 786 ASP cc_start: 0.7630 (t0) cc_final: 0.7428 (t0) outliers start: 53 outliers final: 36 residues processed: 180 average time/residue: 0.1620 time to fit residues: 44.0046 Evaluate side-chains 168 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 758 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 771 THR 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 108 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 307 VAL Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 40.0000 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 9324 Z= 0.324 Angle : 0.634 7.479 12682 Z= 0.332 Chirality : 0.046 0.151 1462 Planarity : 0.005 0.052 1560 Dihedral : 5.560 53.591 1324 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.86 % Allowed : 25.25 % 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: 0.47 (0.25), residues: 1094 helix: 2.03 (0.23), residues: 478 sheet: -0.09 (0.31), residues: 258 loop : -1.81 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 629 HIS 0.004 0.001 HIS B 178 PHE 0.040 0.002 PHE B 317 TYR 0.025 0.002 TYR A 188 ARG 0.002 0.000 ARG A 98 *********************** 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 192 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 134 time to evaluate : 0.931 Fit side-chains REVERT: A 106 TRP cc_start: 0.7374 (p90) cc_final: 0.7058 (p90) REVERT: A 316 ILE cc_start: 0.8437 (pp) cc_final: 0.8198 (pp) REVERT: A 684 MET cc_start: -0.0903 (mmt) cc_final: -0.1869 (ptp) REVERT: A 725 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 786 ASP cc_start: 0.7461 (t0) cc_final: 0.7200 (t0) REVERT: B 106 TRP cc_start: 0.7513 (p90) cc_final: 0.7137 (p90) REVERT: B 317 PHE cc_start: 0.7014 (m-80) cc_final: 0.6804 (m-80) REVERT: B 509 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7876 (t80) REVERT: B 681 MET cc_start: 0.4393 (mmp) cc_final: 0.3103 (mtp) REVERT: B 786 ASP cc_start: 0.7626 (t0) cc_final: 0.7352 (t0) outliers start: 58 outliers final: 43 residues processed: 183 average time/residue: 0.1658 time to fit residues: 45.6296 Evaluate side-chains 173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 103 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 238 GLN Chi-restraints excluded: chain A residue 297 ILE 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 496 ASN Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR 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 108 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 484 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 40.0000 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9324 Z= 0.230 Angle : 0.592 9.780 12682 Z= 0.303 Chirality : 0.044 0.143 1462 Planarity : 0.004 0.051 1560 Dihedral : 5.087 52.664 1324 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.45 % Allowed : 25.86 % Favored : 68.69 % 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: 0.74 (0.26), residues: 1094 helix: 2.26 (0.23), residues: 478 sheet: 0.26 (0.33), residues: 240 loop : -1.79 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.002 0.001 HIS B 229 PHE 0.034 0.002 PHE B 806 TYR 0.019 0.001 TYR A 188 ARG 0.001 0.000 ARG B 289 *********************** 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 195 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 106 TRP cc_start: 0.7394 (p90) cc_final: 0.7159 (p90) REVERT: A 316 ILE cc_start: 0.8223 (pp) cc_final: 0.7979 (pp) REVERT: A 455 TYR cc_start: 0.7786 (t80) cc_final: 0.7561 (t80) REVERT: A 496 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7718 (p0) REVERT: A 684 MET cc_start: -0.0890 (mmt) cc_final: -0.1850 (ptp) REVERT: A 725 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 786 ASP cc_start: 0.7446 (t0) cc_final: 0.7112 (t0) REVERT: B 94 LEU cc_start: 0.5935 (mm) cc_final: 0.5577 (mm) REVERT: B 106 TRP cc_start: 0.7530 (p90) cc_final: 0.7304 (p90) REVERT: B 509 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7736 (t80) REVERT: B 510 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7515 (tt) REVERT: B 580 MET cc_start: 0.6039 (tmm) cc_final: 0.5838 (tmm) REVERT: B 786 ASP cc_start: 0.7432 (t0) cc_final: 0.7117 (t0) outliers start: 54 outliers final: 34 residues processed: 184 average time/residue: 0.1762 time to fit residues: 48.8948 Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 ILE 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 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 721 LEU Chi-restraints excluded: chain A residue 725 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 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 510 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9324 Z= 0.231 Angle : 0.610 9.057 12682 Z= 0.312 Chirality : 0.045 0.161 1462 Planarity : 0.004 0.050 1560 Dihedral : 5.026 51.873 1324 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.95 % Allowed : 26.67 % Favored : 68.38 % 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: 0.71 (0.26), residues: 1094 helix: 2.26 (0.23), residues: 478 sheet: 0.06 (0.32), residues: 258 loop : -1.76 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.002 0.001 HIS A 541 PHE 0.046 0.002 PHE B 317 TYR 0.019 0.001 TYR A 188 ARG 0.002 0.000 ARG B 517 *********************** 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 181 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 190 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.6703 (tp) REVERT: A 496 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7715 (p0) REVERT: A 509 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7912 (t80) REVERT: A 684 MET cc_start: -0.0732 (mmt) cc_final: -0.0966 (mmm) REVERT: A 725 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7737 (mp) REVERT: B 94 LEU cc_start: 0.6221 (mm) cc_final: 0.5924 (mm) REVERT: B 106 TRP cc_start: 0.7582 (p90) cc_final: 0.7375 (p90) REVERT: B 509 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 786 ASP cc_start: 0.7432 (t0) cc_final: 0.7117 (t0) outliers start: 49 outliers final: 36 residues processed: 171 average time/residue: 0.1637 time to fit residues: 42.3152 Evaluate side-chains 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 297 ILE 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 509 PHE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 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 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 758 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9324 Z= 0.288 Angle : 0.639 9.378 12682 Z= 0.327 Chirality : 0.046 0.167 1462 Planarity : 0.004 0.053 1560 Dihedral : 5.081 48.941 1324 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.25 % Allowed : 27.07 % Favored : 67.68 % 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: 0.63 (0.26), residues: 1094 helix: 2.20 (0.23), residues: 478 sheet: 0.02 (0.32), residues: 254 loop : -1.79 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.003 0.001 HIS B 791 PHE 0.033 0.002 PHE B 317 TYR 0.023 0.002 TYR A 188 ARG 0.002 0.000 ARG A 127 *********************** 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 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.6766 (tp) REVERT: A 509 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 725 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 94 LEU cc_start: 0.6328 (mm) cc_final: 0.6025 (mm) REVERT: B 509 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7788 (t80) REVERT: B 786 ASP cc_start: 0.7443 (t0) cc_final: 0.7128 (t0) outliers start: 52 outliers final: 38 residues processed: 177 average time/residue: 0.1604 time to fit residues: 43.1058 Evaluate side-chains 173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 297 ILE 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 496 ASN Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR 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 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 714 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 758 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 0.0670 chunk 92 optimal weight: 9.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 636 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9324 Z= 0.179 Angle : 0.599 10.533 12682 Z= 0.303 Chirality : 0.045 0.187 1462 Planarity : 0.004 0.051 1560 Dihedral : 4.817 42.772 1324 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.65 % Allowed : 27.58 % Favored : 67.78 % 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: 0.82 (0.26), residues: 1094 helix: 2.37 (0.23), residues: 478 sheet: 0.09 (0.32), residues: 250 loop : -1.68 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 106 HIS 0.002 0.000 HIS A 541 PHE 0.056 0.002 PHE A 727 TYR 0.021 0.001 TYR B 116 ARG 0.006 0.000 ARG B 127 *********************** 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: 46 poor density : 140 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.6656 (tp) REVERT: A 316 ILE cc_start: 0.8074 (pp) cc_final: 0.7793 (pp) REVERT: A 509 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7726 (t80) REVERT: A 725 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7637 (mp) REVERT: B 94 LEU cc_start: 0.6186 (mm) cc_final: 0.5986 (mm) REVERT: B 190 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6870 (tp) REVERT: B 496 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7623 (p0) REVERT: B 509 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 786 ASP cc_start: 0.7352 (t0) cc_final: 0.7014 (t0) outliers start: 46 outliers final: 32 residues processed: 177 average time/residue: 0.1638 time to fit residues: 44.3560 Evaluate side-chains 174 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 65 SER 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 173 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 ILE 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 509 PHE 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 725 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 163 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 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 Chi-restraints excluded: chain B residue 758 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 50.0000 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9324 Z= 0.177 Angle : 0.621 13.589 12682 Z= 0.311 Chirality : 0.045 0.209 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.639 40.775 1324 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.24 % Allowed : 28.59 % Favored : 67.17 % 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: 0.85 (0.26), residues: 1094 helix: 2.39 (0.23), residues: 480 sheet: 0.12 (0.32), residues: 250 loop : -1.68 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 106 HIS 0.007 0.001 HIS A 168 PHE 0.042 0.001 PHE B 317 TYR 0.017 0.001 TYR B 455 ARG 0.001 0.000 ARG B 289 *********************** 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 178 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.6650 (tp) REVERT: A 725 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 94 LEU cc_start: 0.6170 (mm) cc_final: 0.5930 (mm) REVERT: B 190 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6849 (tp) REVERT: B 496 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7610 (p0) REVERT: B 509 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7751 (t80) REVERT: B 786 ASP cc_start: 0.7348 (t0) cc_final: 0.7014 (t0) outliers start: 42 outliers final: 30 residues processed: 168 average time/residue: 0.1634 time to fit residues: 41.9246 Evaluate side-chains 172 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 ILE 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 561 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 752 VAL 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 163 VAL Chi-restraints excluded: chain B residue 190 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 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 758 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9324 Z= 0.242 Angle : 0.653 11.726 12682 Z= 0.330 Chirality : 0.046 0.217 1462 Planarity : 0.004 0.051 1560 Dihedral : 4.735 36.540 1324 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.04 % Allowed : 28.48 % Favored : 67.47 % 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: 0.77 (0.26), residues: 1094 helix: 2.28 (0.23), residues: 480 sheet: 0.10 (0.32), residues: 250 loop : -1.69 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.007 0.001 HIS A 168 PHE 0.039 0.002 PHE B 317 TYR 0.030 0.002 TYR B 116 ARG 0.002 0.000 ARG B 98 ********************** 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 170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6734 (tp) REVERT: A 509 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7787 (t80) REVERT: A 725 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B 94 LEU cc_start: 0.6302 (mm) cc_final: 0.6078 (mm) REVERT: B 190 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.6979 (tp) REVERT: B 509 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7832 (t80) REVERT: B 786 ASP cc_start: 0.7418 (t0) cc_final: 0.7085 (t0) outliers start: 40 outliers final: 32 residues processed: 163 average time/residue: 0.1569 time to fit residues: 39.1949 Evaluate side-chains 164 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 ILE 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 509 PHE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 752 VAL 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 163 VAL Chi-restraints excluded: chain B residue 190 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 714 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 758 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4583 r_free = 0.4583 target = 0.212770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157325 restraints weight = 11798.384| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 4.37 r_work: 0.3843 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9324 Z= 0.212 Angle : 0.650 15.368 12682 Z= 0.325 Chirality : 0.047 0.272 1462 Planarity : 0.004 0.051 1560 Dihedral : 4.638 32.737 1324 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.14 % Allowed : 28.18 % Favored : 67.68 % 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: 0.79 (0.26), residues: 1094 helix: 2.33 (0.23), residues: 480 sheet: 0.05 (0.32), residues: 254 loop : -1.69 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 754 HIS 0.006 0.001 HIS A 168 PHE 0.038 0.002 PHE B 317 TYR 0.017 0.001 TYR A 188 ARG 0.001 0.000 ARG B 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1904.32 seconds wall clock time: 35 minutes 41.09 seconds (2141.09 seconds total)