Starting phenix.real_space_refine on Wed Feb 4 07:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxi_61864/02_2026/9jxi_61864.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxi_61864/02_2026/9jxi_61864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jxi_61864/02_2026/9jxi_61864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxi_61864/02_2026/9jxi_61864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jxi_61864/02_2026/9jxi_61864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxi_61864/02_2026/9jxi_61864.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.052 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 40 5.16 5 C 6112 2.51 5 N 1498 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4581 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 16, 'TRANS': 530} Chain breaks: 5 Chain: "B" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4581 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 16, 'TRANS': 530} Chain breaks: 5 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'I8P': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'I8P': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.12, per 1000 atoms: 0.23 Number of scatterers: 9338 At special positions: 0 Unit cell: (100.225, 125.545, 127.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 32 15.00 O 1656 8.00 N 1498 7.00 C 6112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 318.8 milliseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.729A pdb=" N HIS A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 49 through 94 removed outlier: 3.956A pdb=" N SER A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 168 Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.663A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 230 through 257 removed outlier: 3.633A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 294 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.778A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 4.196A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.584A pdb=" N ALA A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.670A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 removed outlier: 4.151A pdb=" N GLN A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 4.213A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.062A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 533 Processing helix chain 'A' and resid 556 through 582 removed outlier: 3.828A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 596 through 618 removed outlier: 3.737A pdb=" N PHE A 602 " --> pdb=" O PRO A 598 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 21 through 34 Processing helix chain 'B' and resid 49 through 94 removed outlier: 3.956A pdb=" N SER B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 168 Processing helix chain 'B' and resid 170 through 180 removed outlier: 3.664A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 206 Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 230 through 257 removed outlier: 3.633A pdb=" N THR B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 294 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.778A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 360 removed outlier: 4.196A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 391 through 397 removed outlier: 3.584A pdb=" N ALA B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.670A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 removed outlier: 4.151A pdb=" N GLN B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 4.213A pdb=" N ARG B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.062A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 485 " --> pdb=" O GLY B 481 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 533 Processing helix chain 'B' and resid 556 through 582 removed outlier: 3.827A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 596 through 618 removed outlier: 3.736A pdb=" N PHE B 602 " --> pdb=" O PRO B 598 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1375 1.31 - 1.44: 2914 1.44 - 1.56: 5221 1.56 - 1.68: 40 1.68 - 1.81: 56 Bond restraints: 9606 Sorted by residual: bond pdb=" O41 I8P A 702 " pdb=" PB1 I8P A 702 " ideal model delta sigma weight residual 1.694 1.602 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O45 I8P A 701 " pdb=" PB5 I8P A 701 " ideal model delta sigma weight residual 1.695 1.603 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O41 I8P B 702 " pdb=" PB1 I8P B 702 " ideal model delta sigma weight residual 1.694 1.603 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" O41 I8P A 701 " pdb=" PB1 I8P A 701 " ideal model delta sigma weight residual 1.694 1.603 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" O45 I8P B 701 " pdb=" PB5 I8P B 701 " ideal model delta sigma weight residual 1.695 1.605 0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 9601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 12911 3.72 - 7.44: 127 7.44 - 11.16: 21 11.16 - 14.88: 3 14.88 - 18.59: 4 Bond angle restraints: 13066 Sorted by residual: angle pdb=" C TYR B 553 " pdb=" CA TYR B 553 " pdb=" CB TYR B 553 " ideal model delta sigma weight residual 108.87 120.26 -11.39 1.41e+00 5.03e-01 6.52e+01 angle pdb=" C TYR A 553 " pdb=" CA TYR A 553 " pdb=" CB TYR A 553 " ideal model delta sigma weight residual 108.87 120.25 -11.38 1.41e+00 5.03e-01 6.52e+01 angle pdb=" N VAL A 182 " pdb=" CA VAL A 182 " pdb=" C VAL A 182 " ideal model delta sigma weight residual 113.20 105.55 7.65 9.60e-01 1.09e+00 6.36e+01 angle pdb=" N VAL B 182 " pdb=" CA VAL B 182 " pdb=" C VAL B 182 " ideal model delta sigma weight residual 113.20 105.62 7.58 9.60e-01 1.09e+00 6.24e+01 angle pdb=" PA1 I8P B 702 " pdb=" O41 I8P B 702 " pdb=" PB1 I8P B 702 " ideal model delta sigma weight residual 146.55 127.96 18.59 3.00e+00 1.11e-01 3.84e+01 ... (remaining 13061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 5166 25.61 - 51.22: 399 51.22 - 76.83: 106 76.83 - 102.44: 23 102.44 - 128.04: 20 Dihedral angle restraints: 5714 sinusoidal: 2470 harmonic: 3244 Sorted by residual: dihedral pdb=" CA THR A 383 " pdb=" C THR A 383 " pdb=" N ALA A 384 " pdb=" CA ALA A 384 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA THR B 383 " pdb=" C THR B 383 " pdb=" N ALA B 384 " pdb=" CA ALA B 384 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA GLN A 399 " pdb=" C GLN A 399 " pdb=" N LEU A 400 " pdb=" CA LEU A 400 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 5711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 1408 1.009 - 2.017: 0 2.017 - 3.026: 0 3.026 - 4.034: 0 4.034 - 5.043: 4 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C3 I8P B 701 " pdb=" C2 I8P B 701 " pdb=" C4 I8P B 701 " pdb=" O13 I8P B 701 " both_signs ideal model delta sigma weight residual False -2.42 2.62 -5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C3 I8P B 702 " pdb=" C2 I8P B 702 " pdb=" C4 I8P B 702 " pdb=" O13 I8P B 702 " both_signs ideal model delta sigma weight residual False -2.42 2.62 -5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C3 I8P A 702 " pdb=" C2 I8P A 702 " pdb=" C4 I8P A 702 " pdb=" O13 I8P A 702 " both_signs ideal model delta sigma weight residual False -2.42 2.62 -5.04 2.00e-01 2.50e+01 6.35e+02 ... (remaining 1409 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 586 " 0.017 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C PRO B 586 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO B 586 " 0.024 2.00e-02 2.50e+03 pdb=" N HIS B 587 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 586 " 0.017 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C PRO A 586 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO A 586 " 0.024 2.00e-02 2.50e+03 pdb=" N HIS A 587 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 552 " -0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C VAL A 552 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL A 552 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR A 553 " -0.021 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 34 2.30 - 2.95: 4842 2.95 - 3.60: 14362 3.60 - 4.25: 21837 4.25 - 4.90: 36528 Nonbonded interactions: 77603 Sorted by model distance: nonbonded pdb=" O LYS B 216 " pdb=" CG2 VAL B 220 " model vdw 1.655 3.460 nonbonded pdb=" O LYS A 216 " pdb=" CG2 VAL A 220 " model vdw 1.656 3.460 nonbonded pdb=" OD1 ASN B 70 " pdb=" CD2 PHE B 185 " model vdw 1.772 3.340 nonbonded pdb=" OD1 ASN A 70 " pdb=" CD2 PHE A 185 " model vdw 1.773 3.340 nonbonded pdb=" O HIS A 587 " pdb=" OG SER A 588 " model vdw 1.956 3.040 ... (remaining 77598 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: 0.01 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 : 0.015 0.815 9611 Z= 1.036 Angle : 1.036 18.595 13070 Z= 0.566 Chirality : 0.272 5.043 1412 Planarity : 0.006 0.070 1570 Dihedral : 21.595 128.045 3604 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.60 % Favored : 91.21 % Rotamer: Outliers : 0.41 % Allowed : 15.91 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.23), residues: 1070 helix: -0.74 (0.16), residues: 852 sheet: None (None), residues: 0 loop : -3.99 (0.33), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 82 TYR 0.028 0.002 TYR B 553 PHE 0.019 0.002 PHE A 372 TRP 0.025 0.003 TRP A 607 HIS 0.005 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.01191 ( 9606) covalent geometry : angle 1.03556 (13066) SS BOND : bond 0.00045 ( 2) SS BOND : angle 1.02618 ( 4) hydrogen bonds : bond 0.11113 ( 642) hydrogen bonds : angle 5.53853 ( 1926) Misc. bond : bond 0.50329 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7824 (mm-30) REVERT: A 199 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6751 (mm-30) REVERT: A 215 MET cc_start: 0.7779 (mmp) cc_final: 0.6999 (tpt) REVERT: A 413 MET cc_start: 0.8402 (ttp) cc_final: 0.8198 (ttt) REVERT: A 527 ILE cc_start: 0.8197 (mm) cc_final: 0.7989 (mt) REVERT: A 600 GLU cc_start: 0.7291 (tt0) cc_final: 0.6479 (pt0) REVERT: B 137 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7917 (mm-30) REVERT: B 199 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6703 (mm-30) REVERT: B 215 MET cc_start: 0.7769 (mmp) cc_final: 0.6971 (tpt) REVERT: B 386 PHE cc_start: 0.8164 (m-10) cc_final: 0.7932 (m-10) REVERT: B 527 ILE cc_start: 0.8242 (mm) cc_final: 0.8026 (mt) REVERT: B 600 GLU cc_start: 0.7363 (tt0) cc_final: 0.6535 (pt0) outliers start: 4 outliers final: 4 residues processed: 130 average time/residue: 0.1151 time to fit residues: 20.1194 Evaluate side-chains 105 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 443 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 248 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS B 10 HIS B 248 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.216144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150600 restraints weight = 9151.317| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.45 r_work: 0.3323 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9611 Z= 0.154 Angle : 0.681 10.418 13070 Z= 0.335 Chirality : 0.043 0.317 1412 Planarity : 0.006 0.076 1570 Dihedral : 20.771 113.589 1472 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.93 % Favored : 95.89 % Rotamer: Outliers : 1.85 % Allowed : 18.17 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.26), residues: 1070 helix: 0.74 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -3.05 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 570 TYR 0.017 0.002 TYR A 368 PHE 0.032 0.001 PHE A 185 TRP 0.021 0.002 TRP A 607 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9606) covalent geometry : angle 0.68073 (13066) SS BOND : bond 0.00288 ( 2) SS BOND : angle 1.21737 ( 4) hydrogen bonds : bond 0.04390 ( 642) hydrogen bonds : angle 4.37927 ( 1926) Misc. bond : bond 0.00128 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7690 (mm-30) REVERT: A 199 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7257 (mm-30) REVERT: A 215 MET cc_start: 0.8530 (mmp) cc_final: 0.7779 (tpt) REVERT: A 366 PHE cc_start: 0.8602 (m-10) cc_final: 0.8219 (m-80) REVERT: A 372 PHE cc_start: 0.7912 (m-80) cc_final: 0.7703 (m-80) REVERT: A 413 MET cc_start: 0.8310 (ttp) cc_final: 0.8101 (ttt) REVERT: A 575 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6518 (tp) REVERT: A 600 GLU cc_start: 0.7711 (tt0) cc_final: 0.6812 (pt0) REVERT: B 28 MET cc_start: 0.8745 (ttm) cc_final: 0.8518 (mtm) REVERT: B 137 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7770 (mm-30) REVERT: B 199 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7243 (mm-30) REVERT: B 215 MET cc_start: 0.8405 (mmp) cc_final: 0.7660 (tpt) REVERT: B 575 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6655 (tp) REVERT: B 600 GLU cc_start: 0.7741 (tt0) cc_final: 0.6842 (pt0) outliers start: 18 outliers final: 8 residues processed: 110 average time/residue: 0.1207 time to fit residues: 17.8929 Evaluate side-chains 91 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 0.0670 chunk 91 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.218259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152373 restraints weight = 9222.159| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.62 r_work: 0.3309 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9611 Z= 0.131 Angle : 0.603 9.450 13070 Z= 0.298 Chirality : 0.041 0.212 1412 Planarity : 0.005 0.053 1570 Dihedral : 19.796 110.535 1468 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.55 % Favored : 96.26 % Rotamer: Outliers : 1.85 % Allowed : 19.92 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1070 helix: 1.47 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.90 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 548 TYR 0.013 0.001 TYR B 368 PHE 0.030 0.001 PHE A 185 TRP 0.015 0.002 TRP A 607 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9606) covalent geometry : angle 0.60301 (13066) SS BOND : bond 0.00227 ( 2) SS BOND : angle 1.03628 ( 4) hydrogen bonds : bond 0.03901 ( 642) hydrogen bonds : angle 4.09586 ( 1926) Misc. bond : bond 0.00175 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.8959 (ttm) cc_final: 0.8529 (mtm) REVERT: A 137 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7634 (mm-30) REVERT: A 215 MET cc_start: 0.8370 (mmp) cc_final: 0.8043 (mmt) REVERT: A 368 TYR cc_start: 0.7748 (t80) cc_final: 0.7423 (t80) REVERT: A 372 PHE cc_start: 0.7875 (m-80) cc_final: 0.7651 (m-80) REVERT: A 413 MET cc_start: 0.8429 (ttp) cc_final: 0.8147 (ttt) REVERT: A 482 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.5908 (pttt) REVERT: A 600 GLU cc_start: 0.7811 (tt0) cc_final: 0.6795 (pt0) REVERT: B 28 MET cc_start: 0.8881 (ttm) cc_final: 0.8547 (mtm) REVERT: B 137 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7699 (mm-30) REVERT: B 168 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8369 (pp20) REVERT: B 186 TYR cc_start: 0.8368 (t80) cc_final: 0.7910 (t80) REVERT: B 199 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7203 (mm-30) REVERT: B 215 MET cc_start: 0.8453 (mmp) cc_final: 0.7690 (tpt) REVERT: B 413 MET cc_start: 0.8288 (ttp) cc_final: 0.7960 (ttt) REVERT: B 482 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.6971 (tttm) REVERT: B 575 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6754 (tp) REVERT: B 600 GLU cc_start: 0.7844 (tt0) cc_final: 0.6822 (pt0) outliers start: 18 outliers final: 9 residues processed: 103 average time/residue: 0.1236 time to fit residues: 17.0740 Evaluate side-chains 92 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.214946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149059 restraints weight = 9276.446| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.46 r_work: 0.3302 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9611 Z= 0.168 Angle : 0.612 9.508 13070 Z= 0.303 Chirality : 0.042 0.232 1412 Planarity : 0.004 0.054 1570 Dihedral : 18.979 109.300 1468 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.02 % Favored : 95.79 % Rotamer: Outliers : 3.18 % Allowed : 20.33 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.26), residues: 1070 helix: 1.60 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.84 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.015 0.001 TYR A 186 PHE 0.026 0.001 PHE A 185 TRP 0.013 0.002 TRP B 607 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9606) covalent geometry : angle 0.61215 (13066) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.85566 ( 4) hydrogen bonds : bond 0.04013 ( 642) hydrogen bonds : angle 4.06853 ( 1926) Misc. bond : bond 0.00119 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7652 (mm-30) REVERT: A 167 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8734 (mm) REVERT: A 199 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6903 (mm-30) REVERT: A 215 MET cc_start: 0.8345 (mmp) cc_final: 0.7903 (mmp) REVERT: A 372 PHE cc_start: 0.7977 (m-80) cc_final: 0.7739 (m-80) REVERT: A 600 GLU cc_start: 0.7795 (tt0) cc_final: 0.6796 (pt0) REVERT: B 28 MET cc_start: 0.8924 (ttm) cc_final: 0.8567 (mtm) REVERT: B 137 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7680 (mm-30) REVERT: B 168 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8211 (pp20) REVERT: B 186 TYR cc_start: 0.8309 (t80) cc_final: 0.7925 (t80) REVERT: B 199 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7119 (mm-30) REVERT: B 215 MET cc_start: 0.8365 (mmp) cc_final: 0.7557 (tpt) REVERT: B 372 PHE cc_start: 0.7972 (m-80) cc_final: 0.7649 (m-80) REVERT: B 600 GLU cc_start: 0.7835 (tt0) cc_final: 0.6819 (pt0) outliers start: 31 outliers final: 15 residues processed: 106 average time/residue: 0.1115 time to fit residues: 16.4665 Evaluate side-chains 101 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 59 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 81 optimal weight: 0.0970 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 399 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.217785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152137 restraints weight = 9169.965| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.44 r_work: 0.3346 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9611 Z= 0.126 Angle : 0.565 9.599 13070 Z= 0.278 Chirality : 0.040 0.194 1412 Planarity : 0.004 0.049 1570 Dihedral : 18.399 108.581 1468 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.08 % Allowed : 20.64 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.27), residues: 1070 helix: 1.93 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -2.58 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 548 TYR 0.010 0.001 TYR A 352 PHE 0.026 0.001 PHE A 185 TRP 0.015 0.001 TRP B 607 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9606) covalent geometry : angle 0.56496 (13066) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.97390 ( 4) hydrogen bonds : bond 0.03633 ( 642) hydrogen bonds : angle 3.95495 ( 1926) Misc. bond : bond 0.00035 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7639 (mm-30) REVERT: A 413 MET cc_start: 0.8446 (ttp) cc_final: 0.8208 (ttt) REVERT: A 417 TYR cc_start: 0.8697 (m-80) cc_final: 0.8474 (m-10) REVERT: A 482 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.6866 (tttm) REVERT: A 600 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6751 (pt0) REVERT: B 28 MET cc_start: 0.8975 (ttm) cc_final: 0.8577 (mtm) REVERT: B 137 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7682 (mm-30) REVERT: B 186 TYR cc_start: 0.8231 (t80) cc_final: 0.7872 (t80) REVERT: B 413 MET cc_start: 0.8368 (ttp) cc_final: 0.8028 (ttt) REVERT: B 482 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.6867 (tttm) REVERT: B 600 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6760 (pt0) outliers start: 30 outliers final: 14 residues processed: 103 average time/residue: 0.1073 time to fit residues: 15.4129 Evaluate side-chains 101 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.217684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152512 restraints weight = 9186.712| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.42 r_work: 0.3335 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9611 Z= 0.140 Angle : 0.580 9.728 13070 Z= 0.286 Chirality : 0.041 0.195 1412 Planarity : 0.004 0.047 1570 Dihedral : 18.070 107.417 1468 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.57 % Allowed : 21.56 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.26), residues: 1070 helix: 2.04 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -2.54 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 548 TYR 0.012 0.001 TYR B 352 PHE 0.026 0.001 PHE A 185 TRP 0.013 0.001 TRP A 607 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9606) covalent geometry : angle 0.58006 (13066) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.87715 ( 4) hydrogen bonds : bond 0.03673 ( 642) hydrogen bonds : angle 3.92907 ( 1926) Misc. bond : bond 0.00030 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7633 (mm-30) REVERT: A 167 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8615 (mm) REVERT: A 199 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7042 (mt-10) REVERT: A 213 LYS cc_start: 0.8110 (tttm) cc_final: 0.7896 (tttp) REVERT: A 215 MET cc_start: 0.8265 (mmp) cc_final: 0.7520 (tpt) REVERT: A 413 MET cc_start: 0.8452 (ttp) cc_final: 0.8207 (ttt) REVERT: A 417 TYR cc_start: 0.8720 (m-80) cc_final: 0.8508 (m-10) REVERT: A 418 SER cc_start: 0.9023 (m) cc_final: 0.8762 (t) REVERT: A 482 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.6743 (tttm) REVERT: A 600 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: B 28 MET cc_start: 0.8999 (ttm) cc_final: 0.8601 (mtm) REVERT: B 137 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7668 (mm-30) REVERT: B 186 TYR cc_start: 0.8223 (t80) cc_final: 0.7875 (t80) REVERT: B 199 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 215 MET cc_start: 0.8299 (mmp) cc_final: 0.7536 (tpt) REVERT: B 482 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.6746 (tttm) REVERT: B 489 MET cc_start: 0.7831 (ttp) cc_final: 0.7470 (ttm) REVERT: B 600 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6737 (pt0) outliers start: 25 outliers final: 16 residues processed: 102 average time/residue: 0.0995 time to fit residues: 14.0694 Evaluate side-chains 105 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 100 optimal weight: 0.0870 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.216523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150348 restraints weight = 9237.524| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.45 r_work: 0.3319 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9611 Z= 0.157 Angle : 0.636 17.907 13070 Z= 0.300 Chirality : 0.042 0.195 1412 Planarity : 0.004 0.048 1570 Dihedral : 17.828 106.366 1468 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.46 % Allowed : 21.15 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1070 helix: 2.06 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -2.48 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 548 TYR 0.013 0.001 TYR A 352 PHE 0.026 0.001 PHE A 185 TRP 0.012 0.001 TRP B 607 HIS 0.002 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9606) covalent geometry : angle 0.63621 (13066) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.85001 ( 4) hydrogen bonds : bond 0.03736 ( 642) hydrogen bonds : angle 3.93879 ( 1926) Misc. bond : bond 0.00152 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7634 (mm-30) REVERT: A 167 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8615 (mm) REVERT: A 213 LYS cc_start: 0.8118 (tttm) cc_final: 0.7915 (tttp) REVERT: A 215 MET cc_start: 0.8263 (mmp) cc_final: 0.7330 (tpt) REVERT: A 372 PHE cc_start: 0.7778 (m-80) cc_final: 0.7541 (m-80) REVERT: A 417 TYR cc_start: 0.8748 (m-80) cc_final: 0.8532 (m-10) REVERT: A 418 SER cc_start: 0.9037 (m) cc_final: 0.8772 (t) REVERT: A 482 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.6743 (tttm) REVERT: A 600 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6686 (pt0) REVERT: B 28 MET cc_start: 0.9021 (ttm) cc_final: 0.8598 (mtm) REVERT: B 137 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7667 (mm-30) REVERT: B 186 TYR cc_start: 0.8219 (t80) cc_final: 0.7894 (t80) REVERT: B 199 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 215 MET cc_start: 0.8277 (mmp) cc_final: 0.7514 (tpt) REVERT: B 482 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.6753 (tttm) REVERT: B 600 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6710 (pt0) outliers start: 24 outliers final: 16 residues processed: 103 average time/residue: 0.0901 time to fit residues: 12.9610 Evaluate side-chains 108 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.217202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.151357 restraints weight = 9160.490| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.49 r_work: 0.3324 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9611 Z= 0.149 Angle : 0.616 14.476 13070 Z= 0.297 Chirality : 0.042 0.203 1412 Planarity : 0.004 0.048 1570 Dihedral : 17.497 104.960 1468 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.77 % Allowed : 20.64 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1070 helix: 2.14 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -2.40 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 548 TYR 0.013 0.001 TYR A 352 PHE 0.026 0.001 PHE A 185 TRP 0.013 0.001 TRP A 607 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9606) covalent geometry : angle 0.61589 (13066) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.84945 ( 4) hydrogen bonds : bond 0.03670 ( 642) hydrogen bonds : angle 3.89958 ( 1926) Misc. bond : bond 0.00120 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7627 (mm-30) REVERT: A 167 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 215 MET cc_start: 0.8240 (mmp) cc_final: 0.7300 (tpt) REVERT: A 417 TYR cc_start: 0.8751 (m-80) cc_final: 0.8533 (m-10) REVERT: A 418 SER cc_start: 0.8975 (m) cc_final: 0.8736 (t) REVERT: A 482 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.6724 (tttm) REVERT: A 600 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: B 28 MET cc_start: 0.8992 (ttm) cc_final: 0.8554 (mtm) REVERT: B 137 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7653 (mm-30) REVERT: B 186 TYR cc_start: 0.8155 (t80) cc_final: 0.7797 (t80) REVERT: B 199 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7011 (mt-10) REVERT: B 215 MET cc_start: 0.8190 (mmp) cc_final: 0.7419 (tpt) REVERT: B 368 TYR cc_start: 0.7487 (t80) cc_final: 0.6896 (t80) REVERT: B 482 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6685 (tttm) REVERT: B 600 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6749 (pt0) outliers start: 27 outliers final: 18 residues processed: 102 average time/residue: 0.1023 time to fit residues: 14.0994 Evaluate side-chains 102 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 10 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.219602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.156924 restraints weight = 9243.271| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.42 r_work: 0.3379 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9611 Z= 0.166 Angle : 0.622 11.815 13070 Z= 0.304 Chirality : 0.042 0.208 1412 Planarity : 0.004 0.044 1570 Dihedral : 17.148 103.021 1466 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.77 % Allowed : 21.46 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1070 helix: 2.17 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -2.41 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 548 TYR 0.014 0.001 TYR A 352 PHE 0.026 0.001 PHE A 185 TRP 0.012 0.001 TRP A 607 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9606) covalent geometry : angle 0.62241 (13066) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.79169 ( 4) hydrogen bonds : bond 0.03762 ( 642) hydrogen bonds : angle 3.93282 ( 1926) Misc. bond : bond 0.00087 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7630 (mm-30) REVERT: A 167 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8589 (mm) REVERT: A 215 MET cc_start: 0.8233 (mmp) cc_final: 0.7290 (tpt) REVERT: A 372 PHE cc_start: 0.7934 (m-80) cc_final: 0.7662 (m-80) REVERT: A 418 SER cc_start: 0.8988 (m) cc_final: 0.8757 (t) REVERT: A 482 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.6786 (tttm) REVERT: A 600 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6720 (pt0) REVERT: B 28 MET cc_start: 0.9054 (ttm) cc_final: 0.8586 (mtm) REVERT: B 137 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7658 (mm-30) REVERT: B 186 TYR cc_start: 0.8107 (t80) cc_final: 0.7743 (t80) REVERT: B 215 MET cc_start: 0.8181 (mmp) cc_final: 0.7223 (tpt) REVERT: B 372 PHE cc_start: 0.7926 (m-80) cc_final: 0.7668 (m-80) REVERT: B 482 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6783 (tttm) REVERT: B 600 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6763 (pt0) outliers start: 27 outliers final: 19 residues processed: 99 average time/residue: 0.1119 time to fit residues: 15.1079 Evaluate side-chains 103 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.220613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159026 restraints weight = 9283.931| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.43 r_work: 0.3392 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9611 Z= 0.154 Angle : 0.615 12.585 13070 Z= 0.301 Chirality : 0.042 0.221 1412 Planarity : 0.004 0.043 1570 Dihedral : 16.858 102.222 1466 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.46 % Allowed : 21.56 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.26), residues: 1070 helix: 2.26 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -2.38 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 548 TYR 0.012 0.001 TYR A 352 PHE 0.028 0.001 PHE A 185 TRP 0.013 0.001 TRP A 607 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9606) covalent geometry : angle 0.61531 (13066) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.81404 ( 4) hydrogen bonds : bond 0.03667 ( 642) hydrogen bonds : angle 3.90913 ( 1926) Misc. bond : bond 0.00081 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7631 (mm-30) REVERT: A 167 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 215 MET cc_start: 0.8193 (mmp) cc_final: 0.7238 (tpt) REVERT: A 372 PHE cc_start: 0.7881 (m-80) cc_final: 0.7645 (m-80) REVERT: A 418 SER cc_start: 0.8983 (m) cc_final: 0.8758 (t) REVERT: A 482 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.6486 (tttt) REVERT: A 600 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6718 (pt0) REVERT: B 28 MET cc_start: 0.9051 (ttm) cc_final: 0.8580 (mtm) REVERT: B 137 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7662 (mm-30) REVERT: B 186 TYR cc_start: 0.8091 (t80) cc_final: 0.7735 (t80) REVERT: B 215 MET cc_start: 0.8165 (mmp) cc_final: 0.7176 (tpt) REVERT: B 372 PHE cc_start: 0.7849 (m-80) cc_final: 0.7592 (m-80) REVERT: B 482 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.6770 (tttm) REVERT: B 508 MET cc_start: 0.6745 (tpt) cc_final: 0.5866 (ttp) REVERT: B 600 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6750 (pt0) outliers start: 24 outliers final: 18 residues processed: 96 average time/residue: 0.0997 time to fit residues: 12.9908 Evaluate side-chains 103 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 32 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.4500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.223366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163837 restraints weight = 9178.306| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.51 r_work: 0.3424 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9611 Z= 0.125 Angle : 0.598 12.838 13070 Z= 0.290 Chirality : 0.041 0.233 1412 Planarity : 0.004 0.042 1570 Dihedral : 16.460 101.246 1464 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.85 % Allowed : 21.66 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.26), residues: 1070 helix: 2.44 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -2.34 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 548 TYR 0.016 0.001 TYR B 368 PHE 0.029 0.001 PHE A 185 TRP 0.016 0.001 TRP A 607 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9606) covalent geometry : angle 0.59743 (13066) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.90945 ( 4) hydrogen bonds : bond 0.03440 ( 642) hydrogen bonds : angle 3.84007 ( 1926) Misc. bond : bond 0.00063 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3073.51 seconds wall clock time: 53 minutes 8.26 seconds (3188.26 seconds total)