Starting phenix.real_space_refine on Mon May 12 14:38:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k13_36785/05_2025/8k13_36785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k13_36785/05_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_36785/05_2025/8k13_36785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k13_36785/05_2025/8k13_36785.map" model { file = "/net/cci-nas-00/data/ceres_data/8k13_36785/05_2025/8k13_36785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k13_36785/05_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-5687/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: 5.92, per 1000 atoms: 0.65 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: 2.49 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: 0.96 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: 2.93 Time building geometry restraints manager: 2.88 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: 0.05 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: 0.310 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.570 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- 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 : 0.923 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: 0.1843 time to fit residues: 55.6920 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 : 1.000 ------------------------------------------------------------------------------- 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 = 0.157021 restraints weight = 11602.150| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 4.02 r_work: 0.3831 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- 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 55.970 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 6) link_NAG-ASN : angle 2.73295 ( 18) hydrogen bonds : bond 0.04482 ( 532) hydrogen bonds : angle 5.22097 ( 1536) SS BOND : bond 0.00466 ( 8) SS BOND : angle 1.39475 ( 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 : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7903 (t0) REVERT: A 316 ILE cc_start: 0.8438 (pp) cc_final: 0.8199 (pp) REVERT: A 455 TYR cc_start: 0.8049 (t80) cc_final: 0.7661 (t80) REVERT: A 580 MET cc_start: 0.5868 (mtt) cc_final: 0.5444 (mtt) REVERT: A 681 MET cc_start: 0.3551 (mmp) cc_final: 0.1693 (ttm) REVERT: A 684 MET cc_start: -0.0621 (mmt) cc_final: -0.1113 (pmm) REVERT: B 106 TRP cc_start: 0.8028 (p90) cc_final: 0.7593 (p90) REVERT: B 117 GLN cc_start: 0.7704 (pp30) cc_final: 0.7278 (pp30) REVERT: B 325 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6848 (pp) REVERT: B 455 TYR cc_start: 0.8165 (t80) cc_final: 0.7937 (t80) REVERT: B 555 GLU cc_start: 0.8804 (tm-30) cc_final: 0.7913 (tp30) REVERT: B 681 MET cc_start: 0.3182 (mmp) cc_final: 0.2151 (ttm) REVERT: B 727 PHE cc_start: 0.7838 (m-10) cc_final: 0.7370 (m-10) REVERT: B 731 MET cc_start: 0.7881 (mmm) cc_final: 0.7179 (ttt) REVERT: B 753 MET cc_start: 0.7996 (mmt) cc_final: 0.7588 (mmt) REVERT: B 769 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: B 778 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8722 (mttm) outliers start: 53 outliers final: 26 residues processed: 185 average time/residue: 0.1548 time to fit residues: 42.9258 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 : 0.901 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 23 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS B 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.218570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.164954 restraints weight = 11680.948| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 4.48 r_work: 0.3888 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9338 Z= 0.120 Angle : 0.563 10.860 12716 Z= 0.288 Chirality : 0.043 0.144 1462 Planarity : 0.003 0.045 1560 Dihedral : 5.900 56.910 1324 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.33 % Allowed : 24.44 % 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: 1.04 (0.25), residues: 1094 helix: 2.47 (0.23), residues: 480 sheet: 0.46 (0.33), residues: 236 loop : -1.60 (0.30), residues: 378 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 0.015 0.001 TYR A 188 ARG 0.002 0.000 ARG A 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 6) link_NAG-ASN : angle 2.51217 ( 18) hydrogen bonds : bond 0.03970 ( 532) hydrogen bonds : angle 4.76323 ( 1536) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.88668 ( 16) covalent geometry : bond 0.00269 ( 9324) covalent geometry : angle 0.55463 (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: 33 poor density : 158 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8121 (t80) cc_final: 0.7374 (t80) REVERT: A 580 MET cc_start: 0.5858 (mtt) cc_final: 0.5370 (mtt) REVERT: A 681 MET cc_start: 0.3481 (mmp) cc_final: 0.2198 (ttm) REVERT: A 684 MET cc_start: -0.0638 (mmt) cc_final: -0.1181 (ptp) REVERT: A 727 PHE cc_start: 0.7808 (m-10) cc_final: 0.7431 (m-10) REVERT: A 731 MET cc_start: 0.8162 (mmm) cc_final: 0.7257 (ttt) REVERT: B 111 LEU cc_start: 0.7571 (mp) cc_final: 0.7195 (tt) REVERT: B 117 GLN cc_start: 0.7722 (pp30) cc_final: 0.7263 (pp30) REVERT: B 451 ILE cc_start: 0.8215 (mm) cc_final: 0.7981 (pt) REVERT: B 455 TYR cc_start: 0.8151 (t80) cc_final: 0.7878 (t80) REVERT: B 517 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6985 (ptm-80) REVERT: B 545 PHE cc_start: 0.7546 (m-10) cc_final: 0.7339 (m-10) REVERT: B 555 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7844 (tp30) REVERT: B 681 MET cc_start: 0.3342 (mmp) cc_final: 0.1915 (mtp) REVERT: B 684 MET cc_start: 0.0210 (mmm) cc_final: -0.0344 (ptp) REVERT: B 727 PHE cc_start: 0.7820 (m-10) cc_final: 0.7372 (m-10) REVERT: B 731 MET cc_start: 0.8189 (mmm) cc_final: 0.7299 (ttt) REVERT: B 753 MET cc_start: 0.8252 (mmt) cc_final: 0.7704 (mmt) outliers start: 33 outliers final: 18 residues processed: 184 average time/residue: 0.1516 time to fit residues: 42.0534 Evaluate side-chains 165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS 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: 7.9990 chunk 42 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 178 HIS ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.207565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150542 restraints weight = 11761.058| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.84 r_work: 0.3775 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 9338 Z= 0.284 Angle : 0.709 8.847 12716 Z= 0.368 Chirality : 0.049 0.160 1462 Planarity : 0.006 0.062 1560 Dihedral : 5.763 52.447 1324 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.66 % Allowed : 23.84 % Favored : 70.51 % 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: 0.46 (0.25), residues: 1094 helix: 2.04 (0.23), residues: 478 sheet: -0.19 (0.31), residues: 258 loop : -1.76 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 629 HIS 0.016 0.002 HIS B 50 PHE 0.021 0.003 PHE A 48 TYR 0.031 0.002 TYR A 188 ARG 0.002 0.000 ARG B 707 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 6) link_NAG-ASN : angle 2.99145 ( 18) hydrogen bonds : bond 0.04630 ( 532) hydrogen bonds : angle 5.32515 ( 1536) SS BOND : bond 0.00425 ( 8) SS BOND : angle 1.08389 ( 16) covalent geometry : bond 0.00685 ( 9324) covalent geometry : angle 0.69965 (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 191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 1.037 Fit side-chains REVERT: A 106 TRP cc_start: 0.8111 (p90) cc_final: 0.7805 (p90) REVERT: A 455 TYR cc_start: 0.8187 (t80) cc_final: 0.7871 (t80) REVERT: A 580 MET cc_start: 0.5840 (mtt) cc_final: 0.5450 (mtt) REVERT: A 684 MET cc_start: -0.1277 (mmt) cc_final: -0.1784 (ptp) REVERT: A 727 PHE cc_start: 0.7916 (m-10) cc_final: 0.7506 (m-80) REVERT: A 731 MET cc_start: 0.8200 (mmm) cc_final: 0.7382 (ttt) REVERT: A 778 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8589 (mttm) REVERT: A 786 ASP cc_start: 0.8206 (t0) cc_final: 0.7939 (t0) REVERT: B 94 LEU cc_start: 0.7392 (mm) cc_final: 0.7068 (mm) REVERT: B 106 TRP cc_start: 0.8101 (p90) cc_final: 0.7721 (p90) REVERT: B 117 GLN cc_start: 0.7930 (pp30) cc_final: 0.7426 (pp30) REVERT: B 317 PHE cc_start: 0.8029 (m-80) cc_final: 0.7688 (m-80) REVERT: B 451 ILE cc_start: 0.8166 (mm) cc_final: 0.7945 (pt) REVERT: B 455 TYR cc_start: 0.8256 (t80) cc_final: 0.7909 (t80) REVERT: B 509 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7873 (t80) REVERT: B 548 MET cc_start: 0.7381 (ptp) cc_final: 0.7173 (ptp) REVERT: B 580 MET cc_start: 0.5370 (mtt) cc_final: 0.5157 (mtt) REVERT: B 681 MET cc_start: 0.3637 (mmp) cc_final: 0.2516 (mtp) REVERT: B 727 PHE cc_start: 0.7910 (m-10) cc_final: 0.7486 (m-80) REVERT: B 731 MET cc_start: 0.8274 (mmm) cc_final: 0.7460 (ttt) REVERT: B 771 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7390 (p) REVERT: B 786 ASP cc_start: 0.8216 (t0) cc_final: 0.7978 (t0) outliers start: 56 outliers final: 38 residues processed: 181 average time/residue: 0.1642 time to fit residues: 44.7619 Evaluate side-chains 171 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 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 564 VAL Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain 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 316 ILE Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 771 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.213197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.157949 restraints weight = 11676.358| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.93 r_work: 0.3846 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9338 Z= 0.141 Angle : 0.591 8.183 12716 Z= 0.301 Chirality : 0.044 0.148 1462 Planarity : 0.004 0.050 1560 Dihedral : 5.162 50.829 1324 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.04 % Allowed : 26.06 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.26), residues: 1094 helix: 2.34 (0.23), residues: 478 sheet: 0.08 (0.32), residues: 254 loop : -1.77 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.002 0.001 HIS A 50 PHE 0.028 0.001 PHE B 806 TYR 0.019 0.001 TYR A 188 ARG 0.001 0.000 ARG B 776 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 6) link_NAG-ASN : angle 2.75241 ( 18) hydrogen bonds : bond 0.03951 ( 532) hydrogen bonds : angle 4.79584 ( 1536) SS BOND : bond 0.00323 ( 8) SS BOND : angle 1.04847 ( 16) covalent geometry : bond 0.00331 ( 9324) covalent geometry : angle 0.58129 (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: 40 poor density : 141 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7329 (mm) cc_final: 0.7074 (mm) REVERT: A 106 TRP cc_start: 0.8103 (p90) cc_final: 0.7534 (p90) REVERT: A 152 MET cc_start: 0.7985 (pmm) cc_final: 0.7738 (pmm) REVERT: A 230 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7643 (t0) REVERT: A 455 TYR cc_start: 0.8173 (t80) cc_final: 0.7848 (t80) REVERT: A 580 MET cc_start: 0.5704 (mtt) cc_final: 0.5296 (mtt) REVERT: A 684 MET cc_start: -0.1280 (mmt) cc_final: -0.1786 (ptp) REVERT: A 725 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8032 (mp) REVERT: A 727 PHE cc_start: 0.7990 (m-10) cc_final: 0.7602 (m-80) REVERT: A 731 MET cc_start: 0.8159 (mmm) cc_final: 0.7354 (ttt) REVERT: A 753 MET cc_start: 0.8720 (mmp) cc_final: 0.7990 (mmt) REVERT: A 778 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8561 (mttm) REVERT: B 94 LEU cc_start: 0.7342 (mm) cc_final: 0.6900 (mm) REVERT: B 106 TRP cc_start: 0.8103 (p90) cc_final: 0.7740 (p90) REVERT: B 111 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7014 (tt) REVERT: B 116 TYR cc_start: 0.8669 (m-80) cc_final: 0.8440 (m-80) REVERT: B 117 GLN cc_start: 0.7818 (pp30) cc_final: 0.7340 (pp30) REVERT: B 317 PHE cc_start: 0.7853 (m-80) cc_final: 0.7548 (m-80) REVERT: B 451 ILE cc_start: 0.8148 (mm) cc_final: 0.7913 (pt) REVERT: B 455 TYR cc_start: 0.8062 (t80) cc_final: 0.7730 (t80) REVERT: B 509 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7699 (t80) REVERT: B 517 ARG cc_start: 0.7340 (tpt170) cc_final: 0.6941 (ptm-80) REVERT: B 548 MET cc_start: 0.7848 (ptp) cc_final: 0.7570 (ptp) REVERT: B 555 GLU cc_start: 0.8747 (tm-30) cc_final: 0.7715 (tp30) REVERT: B 681 MET cc_start: 0.3696 (mmp) cc_final: 0.2593 (mtp) REVERT: B 727 PHE cc_start: 0.8005 (m-10) cc_final: 0.7588 (m-80) REVERT: B 731 MET cc_start: 0.8039 (mmm) cc_final: 0.7453 (ttt) REVERT: B 753 MET cc_start: 0.8726 (mmp) cc_final: 0.8041 (mmt) REVERT: B 786 ASP cc_start: 0.8046 (t0) cc_final: 0.7717 (t0) outliers start: 40 outliers final: 28 residues processed: 175 average time/residue: 0.1619 time to fit residues: 42.4795 Evaluate side-chains 167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 230 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 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 725 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 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 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: 0.9990 chunk 78 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 94 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 40.0000 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.215827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.160311 restraints weight = 11542.329| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 4.08 r_work: 0.3894 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9338 Z= 0.114 Angle : 0.564 8.949 12716 Z= 0.286 Chirality : 0.043 0.153 1462 Planarity : 0.003 0.048 1560 Dihedral : 4.808 47.939 1324 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.34 % Allowed : 26.36 % 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: 0.92 (0.26), residues: 1094 helix: 2.48 (0.23), residues: 478 sheet: 0.16 (0.32), residues: 250 loop : -1.68 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS A 229 PHE 0.027 0.001 PHE B 806 TYR 0.014 0.001 TYR A 188 ARG 0.002 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 6) link_NAG-ASN : angle 2.63247 ( 18) hydrogen bonds : bond 0.03718 ( 532) hydrogen bonds : angle 4.54524 ( 1536) SS BOND : bond 0.00250 ( 8) SS BOND : angle 0.90282 ( 16) covalent geometry : bond 0.00256 ( 9324) covalent geometry : angle 0.55478 (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 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7180 (mm) cc_final: 0.6857 (mm) REVERT: A 106 TRP cc_start: 0.8064 (p90) cc_final: 0.7683 (p90) REVERT: A 152 MET cc_start: 0.7779 (pmm) cc_final: 0.7567 (pmm) REVERT: A 177 PHE cc_start: 0.7897 (t80) cc_final: 0.7305 (t80) REVERT: A 190 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.6833 (tp) REVERT: A 230 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7583 (t0) REVERT: A 445 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.4148 (m-10) REVERT: A 455 TYR cc_start: 0.8019 (t80) cc_final: 0.7617 (t80) REVERT: A 457 LEU cc_start: 0.8865 (mm) cc_final: 0.8636 (mm) REVERT: A 496 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8292 (p0) REVERT: A 580 MET cc_start: 0.5675 (mtt) cc_final: 0.5206 (mtt) REVERT: A 684 MET cc_start: -0.1116 (mmt) cc_final: -0.1592 (ptp) REVERT: A 727 PHE cc_start: 0.7995 (m-10) cc_final: 0.7600 (m-80) REVERT: A 731 MET cc_start: 0.8001 (mmm) cc_final: 0.7432 (ttt) REVERT: A 759 TYR cc_start: 0.7664 (t80) cc_final: 0.7312 (t80) REVERT: A 778 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8545 (mttm) REVERT: A 783 ILE cc_start: 0.8296 (tt) cc_final: 0.7916 (tp) REVERT: B 94 LEU cc_start: 0.7140 (mm) cc_final: 0.6818 (mm) REVERT: B 106 TRP cc_start: 0.8106 (p90) cc_final: 0.7758 (p90) REVERT: B 111 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7190 (tt) REVERT: B 116 TYR cc_start: 0.8665 (m-80) cc_final: 0.8385 (m-80) REVERT: B 117 GLN cc_start: 0.7818 (pp30) cc_final: 0.7369 (pp30) REVERT: B 317 PHE cc_start: 0.7837 (m-80) cc_final: 0.7584 (m-80) REVERT: B 445 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.4005 (m-10) REVERT: B 451 ILE cc_start: 0.8093 (mm) cc_final: 0.7868 (pt) REVERT: B 455 TYR cc_start: 0.7987 (t80) cc_final: 0.7430 (t80) REVERT: B 496 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8253 (p0) REVERT: B 509 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7717 (t80) REVERT: B 517 ARG cc_start: 0.7293 (tpt170) cc_final: 0.6893 (ptm-80) REVERT: B 555 GLU cc_start: 0.8627 (tm-30) cc_final: 0.7560 (tp30) REVERT: B 580 MET cc_start: 0.5696 (mtt) cc_final: 0.5430 (mtt) REVERT: B 727 PHE cc_start: 0.8066 (m-10) cc_final: 0.7757 (m-10) REVERT: B 731 MET cc_start: 0.8082 (mmm) cc_final: 0.7555 (ttt) REVERT: B 753 MET cc_start: 0.8672 (mmp) cc_final: 0.7954 (mmt) REVERT: B 786 ASP cc_start: 0.7930 (t0) cc_final: 0.7553 (t0) outliers start: 43 outliers final: 24 residues processed: 179 average time/residue: 0.1549 time to fit residues: 41.8652 Evaluate side-chains 172 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain A residue 230 ASN 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 496 ASN 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 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 173 THR 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 544 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 721 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 0.0470 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 230 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.214385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.159034 restraints weight = 11745.647| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 4.09 r_work: 0.3874 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9338 Z= 0.135 Angle : 0.579 9.861 12716 Z= 0.291 Chirality : 0.044 0.165 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.647 42.774 1324 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.05 % Allowed : 26.06 % 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: 2.50 (0.23), residues: 478 sheet: 0.17 (0.32), residues: 254 loop : -1.64 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.003 0.001 HIS B 636 PHE 0.024 0.001 PHE B 700 TYR 0.017 0.001 TYR A 188 ARG 0.001 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 2.74112 ( 18) hydrogen bonds : bond 0.03729 ( 532) hydrogen bonds : angle 4.53423 ( 1536) SS BOND : bond 0.00274 ( 8) SS BOND : angle 0.85108 ( 16) covalent geometry : bond 0.00318 ( 9324) covalent geometry : angle 0.57019 (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 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7169 (mm) cc_final: 0.6840 (mm) REVERT: A 106 TRP cc_start: 0.8097 (p90) cc_final: 0.7693 (p90) REVERT: A 152 MET cc_start: 0.7822 (pmm) cc_final: 0.7498 (pmm) REVERT: A 230 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7744 (t0) REVERT: A 445 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.4163 (m-10) REVERT: A 455 TYR cc_start: 0.8020 (t80) cc_final: 0.7751 (t80) REVERT: A 457 LEU cc_start: 0.8954 (mm) cc_final: 0.8640 (mm) REVERT: A 496 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8284 (p0) REVERT: A 580 MET cc_start: 0.5669 (mtt) cc_final: 0.5289 (mtt) REVERT: A 684 MET cc_start: -0.1082 (mmt) cc_final: -0.1587 (ptp) REVERT: A 727 PHE cc_start: 0.7986 (m-10) cc_final: 0.7597 (m-80) REVERT: A 731 MET cc_start: 0.8110 (mmm) cc_final: 0.7500 (ttt) REVERT: A 753 MET cc_start: 0.8681 (mmp) cc_final: 0.8067 (mmt) REVERT: A 778 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8553 (mttm) REVERT: B 94 LEU cc_start: 0.7170 (mm) cc_final: 0.6831 (mm) REVERT: B 106 TRP cc_start: 0.8090 (p90) cc_final: 0.7859 (p90) REVERT: B 111 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7104 (tt) REVERT: B 116 TYR cc_start: 0.8692 (m-80) cc_final: 0.8378 (m-80) REVERT: B 117 GLN cc_start: 0.7838 (pp30) cc_final: 0.7392 (pp30) REVERT: B 451 ILE cc_start: 0.8100 (mm) cc_final: 0.7885 (pt) REVERT: B 455 TYR cc_start: 0.7932 (t80) cc_final: 0.7627 (t80) REVERT: B 496 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8263 (p0) REVERT: B 509 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 517 ARG cc_start: 0.7238 (tpt170) cc_final: 0.6855 (ptm-80) REVERT: B 555 GLU cc_start: 0.8628 (tm-30) cc_final: 0.7574 (tp30) REVERT: B 727 PHE cc_start: 0.8027 (m-10) cc_final: 0.7726 (m-10) REVERT: B 731 MET cc_start: 0.8052 (mmm) cc_final: 0.7569 (ttt) REVERT: B 753 MET cc_start: 0.8732 (mmp) cc_final: 0.8046 (mmt) outliers start: 50 outliers final: 35 residues processed: 176 average time/residue: 0.1548 time to fit residues: 41.1319 Evaluate side-chains 177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 230 ASN 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 557 VAL 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 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 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 771 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.212644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.157361 restraints weight = 11939.712| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 4.14 r_work: 0.3858 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9338 Z= 0.163 Angle : 0.619 10.629 12716 Z= 0.311 Chirality : 0.045 0.216 1462 Planarity : 0.004 0.049 1560 Dihedral : 4.606 35.391 1324 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.76 % Allowed : 25.45 % Favored : 68.79 % 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: 0.89 (0.26), residues: 1094 helix: 2.41 (0.23), residues: 480 sheet: 0.14 (0.32), residues: 254 loop : -1.66 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 629 HIS 0.004 0.001 HIS A 229 PHE 0.053 0.002 PHE A 700 TYR 0.019 0.001 TYR B 188 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 6) link_NAG-ASN : angle 2.82982 ( 18) hydrogen bonds : bond 0.03888 ( 532) hydrogen bonds : angle 4.64635 ( 1536) SS BOND : bond 0.00303 ( 8) SS BOND : angle 0.86466 ( 16) covalent geometry : bond 0.00393 ( 9324) covalent geometry : angle 0.61015 (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 194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 137 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7212 (mm) cc_final: 0.6838 (mm) REVERT: A 106 TRP cc_start: 0.8118 (p90) cc_final: 0.7756 (p90) REVERT: A 152 MET cc_start: 0.7847 (pmm) cc_final: 0.7561 (pmm) REVERT: A 190 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.6986 (tp) REVERT: A 455 TYR cc_start: 0.8075 (t80) cc_final: 0.7816 (t80) REVERT: A 457 LEU cc_start: 0.8992 (mm) cc_final: 0.8656 (mm) REVERT: A 509 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7866 (t80) REVERT: A 548 MET cc_start: 0.7321 (ptp) cc_final: 0.6852 (pmm) REVERT: A 580 MET cc_start: 0.5654 (mtt) cc_final: 0.5383 (mtt) REVERT: A 727 PHE cc_start: 0.8013 (m-10) cc_final: 0.7642 (m-80) REVERT: A 731 MET cc_start: 0.8019 (mmm) cc_final: 0.7468 (ttt) REVERT: A 753 MET cc_start: 0.8727 (mmp) cc_final: 0.8026 (mmt) REVERT: A 778 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8562 (mttm) REVERT: B 94 LEU cc_start: 0.7267 (mm) cc_final: 0.6825 (mm) REVERT: B 106 TRP cc_start: 0.8109 (p90) cc_final: 0.7802 (p90) REVERT: B 117 GLN cc_start: 0.7843 (pp30) cc_final: 0.7396 (pp30) REVERT: B 451 ILE cc_start: 0.8108 (mm) cc_final: 0.7896 (pt) REVERT: B 455 TYR cc_start: 0.8022 (t80) cc_final: 0.7784 (t80) REVERT: B 509 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7718 (t80) REVERT: B 517 ARG cc_start: 0.7252 (tpt170) cc_final: 0.6856 (ptm-80) REVERT: B 555 GLU cc_start: 0.8658 (tm-30) cc_final: 0.7633 (tp30) REVERT: B 727 PHE cc_start: 0.8041 (m-10) cc_final: 0.7799 (m-10) REVERT: B 731 MET cc_start: 0.8052 (mmm) cc_final: 0.7583 (ttt) REVERT: B 786 ASP cc_start: 0.7942 (t0) cc_final: 0.7583 (t0) outliers start: 57 outliers final: 39 residues processed: 180 average time/residue: 0.1551 time to fit residues: 42.3892 Evaluate side-chains 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 230 ASN 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 509 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 721 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 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 771 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.211908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.157530 restraints weight = 11727.655| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.90 r_work: 0.3864 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9338 Z= 0.168 Angle : 0.634 11.774 12716 Z= 0.318 Chirality : 0.045 0.200 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.569 28.391 1324 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.25 % Allowed : 25.45 % 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: 0.84 (0.26), residues: 1094 helix: 2.37 (0.23), residues: 480 sheet: 0.06 (0.32), residues: 258 loop : -1.67 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.005 0.001 HIS A 229 PHE 0.053 0.002 PHE A 700 TYR 0.020 0.001 TYR A 188 ARG 0.002 0.000 ARG A 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 6) link_NAG-ASN : angle 2.89081 ( 18) hydrogen bonds : bond 0.03908 ( 532) hydrogen bonds : angle 4.66475 ( 1536) SS BOND : bond 0.00304 ( 8) SS BOND : angle 0.84856 ( 16) covalent geometry : bond 0.00404 ( 9324) covalent geometry : angle 0.62457 (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 187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7403 (mm) cc_final: 0.7061 (mm) REVERT: A 106 TRP cc_start: 0.8167 (p90) cc_final: 0.7963 (p90) REVERT: A 152 MET cc_start: 0.7837 (pmm) cc_final: 0.7539 (pmm) REVERT: A 190 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.6945 (tp) REVERT: A 230 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7720 (t0) REVERT: A 455 TYR cc_start: 0.8082 (t80) cc_final: 0.7825 (t80) REVERT: A 509 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7799 (t80) REVERT: A 548 MET cc_start: 0.7612 (ptp) cc_final: 0.7326 (pmm) REVERT: A 727 PHE cc_start: 0.7993 (m-10) cc_final: 0.7631 (m-80) REVERT: A 731 MET cc_start: 0.8005 (mmm) cc_final: 0.7483 (ttt) REVERT: A 753 MET cc_start: 0.8723 (mmp) cc_final: 0.8025 (mmt) REVERT: A 778 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8528 (mttm) REVERT: B 94 LEU cc_start: 0.7370 (mm) cc_final: 0.6967 (mm) REVERT: B 106 TRP cc_start: 0.8113 (p90) cc_final: 0.7805 (p90) REVERT: B 116 TYR cc_start: 0.8685 (m-80) cc_final: 0.8358 (m-80) REVERT: B 117 GLN cc_start: 0.7805 (pp30) cc_final: 0.7361 (pp30) REVERT: B 451 ILE cc_start: 0.8099 (mm) cc_final: 0.7872 (pt) REVERT: B 455 TYR cc_start: 0.8044 (t80) cc_final: 0.7761 (t80) REVERT: B 509 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7708 (t80) REVERT: B 517 ARG cc_start: 0.7249 (tpt170) cc_final: 0.6890 (ptm-80) REVERT: B 555 GLU cc_start: 0.8694 (tm-30) cc_final: 0.7691 (tp30) REVERT: B 727 PHE cc_start: 0.8016 (m-10) cc_final: 0.7786 (m-10) REVERT: B 731 MET cc_start: 0.8042 (mmm) cc_final: 0.7595 (ttt) REVERT: B 753 MET cc_start: 0.8687 (mmp) cc_final: 0.8091 (mmt) REVERT: B 786 ASP cc_start: 0.7959 (t0) cc_final: 0.7554 (t0) outliers start: 52 outliers final: 41 residues processed: 176 average time/residue: 0.1532 time to fit residues: 40.8439 Evaluate side-chains 178 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 230 ASN 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 509 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 584 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain 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 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 771 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** 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 = 0.4522 r_free = 0.4522 target = 0.206133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.150292 restraints weight = 12034.040| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.87 r_work: 0.3759 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 9338 Z= 0.318 Angle : 0.781 13.104 12716 Z= 0.396 Chirality : 0.051 0.270 1462 Planarity : 0.006 0.073 1560 Dihedral : 5.352 25.583 1324 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.25 % Allowed : 25.56 % 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: 0.33 (0.26), residues: 1094 helix: 1.92 (0.23), residues: 480 sheet: -0.15 (0.32), residues: 258 loop : -1.92 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 794 HIS 0.006 0.001 HIS A 229 PHE 0.054 0.003 PHE A 700 TYR 0.032 0.002 TYR B 188 ARG 0.005 0.001 ARG A 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 6) link_NAG-ASN : angle 3.41823 ( 18) hydrogen bonds : bond 0.04611 ( 532) hydrogen bonds : angle 5.31284 ( 1536) SS BOND : bond 0.00474 ( 8) SS BOND : angle 1.05019 ( 16) covalent geometry : bond 0.00762 ( 9324) covalent geometry : angle 0.77076 (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 186 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.930 Fit side-chains REVERT: A 106 TRP cc_start: 0.8210 (p90) cc_final: 0.7869 (p90) REVERT: A 190 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7027 (tp) REVERT: A 222 CYS cc_start: 0.6778 (p) cc_final: 0.6353 (p) REVERT: A 509 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 727 PHE cc_start: 0.8012 (m-10) cc_final: 0.7645 (m-80) REVERT: A 731 MET cc_start: 0.8025 (mmm) cc_final: 0.7575 (ttt) REVERT: A 753 MET cc_start: 0.8738 (mmp) cc_final: 0.8099 (mmt) REVERT: A 778 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8512 (mttm) REVERT: B 116 TYR cc_start: 0.8687 (m-80) cc_final: 0.8294 (m-80) REVERT: B 117 GLN cc_start: 0.7858 (pp30) cc_final: 0.7371 (pp30) REVERT: B 451 ILE cc_start: 0.7986 (mm) cc_final: 0.7768 (pt) REVERT: B 509 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7882 (t80) REVERT: B 727 PHE cc_start: 0.8035 (m-10) cc_final: 0.7711 (m-10) REVERT: B 731 MET cc_start: 0.8075 (mmm) cc_final: 0.7605 (ttt) REVERT: B 753 MET cc_start: 0.8691 (mmp) cc_final: 0.8155 (mmt) REVERT: B 771 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7545 (p) REVERT: B 786 ASP cc_start: 0.8166 (t0) cc_final: 0.7817 (t0) REVERT: B 793 ILE cc_start: 0.8967 (mt) cc_final: 0.8728 (mp) outliers start: 52 outliers final: 37 residues processed: 177 average time/residue: 0.1525 time to fit residues: 40.9162 Evaluate side-chains 166 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 230 ASN 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 484 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 509 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 771 THR Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 584 LEU 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 771 THR 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: 0.6980 chunk 41 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** 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** B 636 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.213021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.159094 restraints weight = 11735.219| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.85 r_work: 0.3866 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4036 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= 0.130 Angle : 0.655 13.258 12716 Z= 0.325 Chirality : 0.047 0.345 1462 Planarity : 0.004 0.050 1560 Dihedral : 4.675 25.462 1324 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.84 % Allowed : 26.97 % 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: 0.82 (0.26), residues: 1094 helix: 2.38 (0.23), residues: 480 sheet: 0.18 (0.32), residues: 250 loop : -1.78 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.003 0.001 HIS A 168 PHE 0.050 0.001 PHE A 700 TYR 0.019 0.001 TYR A 188 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 6) link_NAG-ASN : angle 2.98617 ( 18) hydrogen bonds : bond 0.03899 ( 532) hydrogen bonds : angle 4.66351 ( 1536) SS BOND : bond 0.00299 ( 8) SS BOND : angle 1.21484 ( 16) covalent geometry : bond 0.00302 ( 9324) covalent geometry : angle 0.64492 (12682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4657.02 seconds wall clock time: 81 minutes 12.73 seconds (4872.73 seconds total)