Starting phenix.real_space_refine on Sat Aug 23 10:01:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7a_28899/08_2025/8f7a_28899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7a_28899/08_2025/8f7a_28899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7a_28899/08_2025/8f7a_28899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7a_28899/08_2025/8f7a_28899.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7a_28899/08_2025/8f7a_28899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7a_28899/08_2025/8f7a_28899.cif" } resolution = 3.78 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5465 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 4335 2.51 5 N 1119 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6742 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5332 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 5327 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 683, 5327 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 5431 Chain: "B" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1377 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 6, 'TRANS': 162} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.99, per 1000 atoms: 0.44 Number of scatterers: 6742 At special positions: 0 Unit cell: (76.167, 97.092, 104.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 3 15.00 Mg 1 11.99 O 1246 8.00 N 1119 7.00 C 4335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 616.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 2 sheets defined 72.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.642A pdb=" N ASP A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.871A pdb=" N GLU A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 removed outlier: 3.790A pdb=" N TRP A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 4.071A pdb=" N MET A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 Processing helix chain 'A' and resid 181 through 199 Proline residue: A 187 - end of helix Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 204 through 229 Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.527A pdb=" N GLN A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 279 Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.849A pdb=" N MET A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 309 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 329 through 344 Processing helix chain 'A' and resid 346 through 356 removed outlier: 4.301A pdb=" N SER A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 4.156A pdb=" N TYR A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 381 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 397 through 413 removed outlier: 3.566A pdb=" N PHE A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 438 removed outlier: 3.627A pdb=" N SER A 438 " --> pdb=" O GLN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 removed outlier: 4.125A pdb=" N HIS A 447 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 467 removed outlier: 3.810A pdb=" N ILE A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.537A pdb=" N ASN A 487 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 505 removed outlier: 3.624A pdb=" N LEU A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG A 504 " --> pdb=" O TRP A 500 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 510 through 523 Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 530 through 552 removed outlier: 3.717A pdb=" N LYS A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 559 removed outlier: 3.748A pdb=" N GLN A 558 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Proline residue: A 559 - end of helix Processing helix chain 'A' and resid 560 through 573 Processing helix chain 'A' and resid 577 through 594 removed outlier: 4.402A pdb=" N GLU A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP A 594 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 616 removed outlier: 3.634A pdb=" N THR A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) Proline residue: A 607 - end of helix Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.677A pdb=" N GLN A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 639 through 657 Proline residue: A 649 - end of helix Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.537A pdb=" N ILE A 690 " --> pdb=" O SER A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.955A pdb=" N LYS B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 102' Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.343A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 172 Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.715A pdb=" N LEU B 15 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 65 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 67 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 48 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.715A pdb=" N LEU B 15 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1194 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: 1.05 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2152 1.34 - 1.46: 1293 1.46 - 1.57: 3379 1.57 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 6889 Sorted by residual: bond pdb=" CA TRP B 66 " pdb=" CB TRP B 66 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.51e-02 4.39e+03 1.77e+00 bond pdb=" CA THR B 137 " pdb=" CB THR B 137 " ideal model delta sigma weight residual 1.534 1.513 0.021 1.78e-02 3.16e+03 1.36e+00 bond pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta sigma weight residual 1.466 1.452 0.015 1.36e-02 5.41e+03 1.16e+00 bond pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 1.528 1.514 0.014 1.33e-02 5.65e+03 1.07e+00 bond pdb=" CB TRP B 66 " pdb=" CG TRP B 66 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 ... (remaining 6884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 9062 1.57 - 3.14: 251 3.14 - 4.71: 43 4.71 - 6.27: 15 6.27 - 7.84: 5 Bond angle restraints: 9376 Sorted by residual: angle pdb=" C THR B 139 " pdb=" N PHE B 140 " pdb=" CA PHE B 140 " ideal model delta sigma weight residual 122.09 116.56 5.53 1.79e+00 3.12e-01 9.53e+00 angle pdb=" N ILE A 237 " pdb=" CA ILE A 237 " pdb=" C ILE A 237 " ideal model delta sigma weight residual 109.34 115.13 -5.79 2.08e+00 2.31e-01 7.74e+00 angle pdb=" N LYS B 136 " pdb=" CA LYS B 136 " pdb=" C LYS B 136 " ideal model delta sigma weight residual 113.01 109.68 3.33 1.20e+00 6.94e-01 7.70e+00 angle pdb=" C1' GTP B 302 " pdb=" O4' GTP B 302 " pdb=" C4' GTP B 302 " ideal model delta sigma weight residual 111.80 103.96 7.84 3.00e+00 1.11e-01 6.83e+00 angle pdb=" C2' GTP B 302 " pdb=" C1' GTP B 302 " pdb=" N9 GTP B 302 " ideal model delta sigma weight residual 109.47 117.16 -7.69 3.00e+00 1.11e-01 6.57e+00 ... (remaining 9371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3730 17.52 - 35.03: 283 35.03 - 52.55: 93 52.55 - 70.06: 26 70.06 - 87.58: 7 Dihedral angle restraints: 4139 sinusoidal: 1631 harmonic: 2508 Sorted by residual: dihedral pdb=" CA ASN B 158 " pdb=" C ASN B 158 " pdb=" N PHE B 159 " pdb=" CA PHE B 159 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 236 " pdb=" C LEU A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ALA A 143 " pdb=" C ALA A 143 " pdb=" N TRP A 144 " pdb=" CA TRP A 144 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 929 0.055 - 0.110: 160 0.110 - 0.165: 11 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1102 Sorted by residual: chirality pdb=" C1' GTP B 302 " pdb=" C2' GTP B 302 " pdb=" N9 GTP B 302 " pdb=" O4' GTP B 302 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2' GTP B 302 " pdb=" C1' GTP B 302 " pdb=" C3' GTP B 302 " pdb=" O2' GTP B 302 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" C3' GTP B 302 " pdb=" C2' GTP B 302 " pdb=" C4' GTP B 302 " pdb=" O3' GTP B 302 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1099 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 144 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 145 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 238 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 239 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 682 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A 683 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 683 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 683 " 0.020 5.00e-02 4.00e+02 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 2 1.85 - 2.61: 123 2.61 - 3.37: 9904 3.37 - 4.14: 15648 4.14 - 4.90: 29120 Nonbonded interactions: 54797 Sorted by model distance: nonbonded pdb=" OG1 THR B 26 " pdb="MG MG B 301 " model vdw 1.085 2.170 nonbonded pdb="MG MG B 301 " pdb=" O3G GTP B 302 " model vdw 1.776 2.170 nonbonded pdb=" O PHE A 613 " pdb=" OG SER A 617 " model vdw 2.159 3.040 nonbonded pdb=" O PHE A 197 " pdb=" NH1 ARG A 208 " model vdw 2.162 3.120 nonbonded pdb=" OD2 ASP B 93 " pdb=" OG1 THR B 95 " model vdw 2.190 3.040 ... (remaining 54792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 : 0.005 0.046 6889 Z= 0.231 Angle : 0.692 7.842 9376 Z= 0.387 Chirality : 0.041 0.275 1102 Planarity : 0.004 0.042 1177 Dihedral : 15.306 87.575 2501 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 11.80 % Allowed : 9.50 % Favored : 78.70 % 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 aren not related in a simple way. whole: -2.21 (0.27), residues: 843 helix: -0.71 (0.21), residues: 545 sheet: -4.45 (0.50), residues: 47 loop : -2.26 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 168 TYR 0.015 0.001 TYR B 148 PHE 0.014 0.001 PHE B 140 TRP 0.008 0.001 TRP A 144 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 6889) covalent geometry : angle 0.69220 ( 9376) hydrogen bonds : bond 0.16283 ( 398) hydrogen bonds : angle 6.73733 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 223 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8358 (mt0) cc_final: 0.7927 (mt0) REVERT: A 182 MET cc_start: 0.8721 (ttp) cc_final: 0.8476 (ttt) REVERT: A 205 ILE cc_start: 0.8172 (pt) cc_final: 0.7759 (pt) REVERT: A 221 MET cc_start: 0.9070 (ttt) cc_final: 0.8648 (ttt) REVERT: A 279 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6878 (p90) REVERT: A 338 GLU cc_start: 0.7876 (tt0) cc_final: 0.7624 (tp30) REVERT: A 375 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7730 (mt) REVERT: A 499 LEU cc_start: 0.9111 (mt) cc_final: 0.8711 (mt) REVERT: A 515 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: A 516 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8190 (mt0) REVERT: A 541 ILE cc_start: 0.8711 (mt) cc_final: 0.8462 (mt) REVERT: A 717 LEU cc_start: 0.9214 (mm) cc_final: 0.8953 (mm) REVERT: A 720 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: B 91 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4142 (ttt) REVERT: B 131 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.3581 (mtm-85) REVERT: B 139 THR cc_start: 0.6653 (t) cc_final: 0.6382 (t) outliers start: 87 outliers final: 20 residues processed: 280 average time/residue: 0.0846 time to fit residues: 31.7608 Evaluate side-chains 173 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 384 GLN A 414 GLN A 434 GLN A 447 HIS A 515 GLN A 644 GLN A 692 GLN A 712 ASN B 107 HIS B 116 ASN B 147 GLN B 156 ASN B 158 ASN B 175 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086013 restraints weight = 24228.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.090696 restraints weight = 10870.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092911 restraints weight = 6615.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093381 restraints weight = 5695.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093548 restraints weight = 5270.785| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6889 Z= 0.171 Angle : 0.770 7.731 9376 Z= 0.393 Chirality : 0.045 0.249 1102 Planarity : 0.005 0.043 1177 Dihedral : 8.608 61.831 961 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.56 % Allowed : 20.35 % Favored : 74.08 % 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 aren not related in a simple way. whole: -0.47 (0.29), residues: 843 helix: 0.63 (0.22), residues: 537 sheet: -3.22 (0.68), residues: 40 loop : -1.68 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 40 TYR 0.012 0.002 TYR B 100 PHE 0.027 0.002 PHE A 334 TRP 0.014 0.001 TRP B 66 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6889) covalent geometry : angle 0.77001 ( 9376) hydrogen bonds : bond 0.04534 ( 398) hydrogen bonds : angle 4.90266 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8614 (mmm) cc_final: 0.8318 (tpp) REVERT: A 214 ILE cc_start: 0.8383 (mt) cc_final: 0.7980 (mt) REVERT: A 221 MET cc_start: 0.8982 (ttt) cc_final: 0.8747 (ttt) REVERT: A 338 GLU cc_start: 0.8208 (tt0) cc_final: 0.7939 (tp30) REVERT: A 451 MET cc_start: 0.8338 (mtt) cc_final: 0.8087 (mtt) REVERT: A 454 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8193 (mm) REVERT: A 720 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: B 53 SER cc_start: 0.8858 (m) cc_final: 0.8587 (t) REVERT: B 148 TYR cc_start: 0.7894 (t80) cc_final: 0.6838 (t80) outliers start: 41 outliers final: 24 residues processed: 195 average time/residue: 0.0705 time to fit residues: 19.4719 Evaluate side-chains 165 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088874 restraints weight = 13588.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092184 restraints weight = 8265.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.094275 restraints weight = 6129.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095535 restraints weight = 5111.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096456 restraints weight = 4587.151| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6889 Z= 0.155 Angle : 0.744 9.860 9376 Z= 0.370 Chirality : 0.045 0.291 1102 Planarity : 0.004 0.040 1177 Dihedral : 7.080 61.103 938 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.34 % Allowed : 22.52 % Favored : 73.13 % 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 aren not related in a simple way. whole: -0.12 (0.29), residues: 843 helix: 0.86 (0.23), residues: 540 sheet: -3.54 (0.60), residues: 46 loop : -1.30 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 40 TYR 0.010 0.001 TYR A 544 PHE 0.023 0.001 PHE B 37 TRP 0.007 0.001 TRP B 66 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6889) covalent geometry : angle 0.74446 ( 9376) hydrogen bonds : bond 0.04384 ( 398) hydrogen bonds : angle 4.63959 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7524 (pt0) cc_final: 0.7323 (pt0) REVERT: A 97 ARG cc_start: 0.8333 (mmt90) cc_final: 0.7795 (mmt180) REVERT: A 212 VAL cc_start: 0.8632 (t) cc_final: 0.8061 (p) REVERT: A 338 GLU cc_start: 0.8380 (tt0) cc_final: 0.8114 (tp30) REVERT: A 451 MET cc_start: 0.8427 (mtt) cc_final: 0.8188 (mtt) REVERT: A 454 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8500 (mm) REVERT: A 720 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.7475 (m-80) outliers start: 32 outliers final: 19 residues processed: 165 average time/residue: 0.0742 time to fit residues: 17.0071 Evaluate side-chains 146 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087216 restraints weight = 24639.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090620 restraints weight = 11520.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.091826 restraints weight = 7710.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092619 restraints weight = 6820.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092744 restraints weight = 6243.996| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6889 Z= 0.170 Angle : 0.759 9.141 9376 Z= 0.377 Chirality : 0.045 0.282 1102 Planarity : 0.004 0.039 1177 Dihedral : 6.843 64.365 929 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.61 % Allowed : 23.61 % Favored : 71.78 % 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 aren not related in a simple way. whole: -0.09 (0.29), residues: 843 helix: 0.79 (0.22), residues: 542 sheet: -2.83 (0.70), residues: 40 loop : -1.28 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 40 TYR 0.009 0.001 TYR B 148 PHE 0.025 0.002 PHE A 238 TRP 0.022 0.001 TRP A 144 HIS 0.008 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6889) covalent geometry : angle 0.75886 ( 9376) hydrogen bonds : bond 0.04438 ( 398) hydrogen bonds : angle 4.62478 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8549 (mmt90) cc_final: 0.8085 (mmt180) REVERT: A 221 MET cc_start: 0.8951 (ttt) cc_final: 0.8692 (ttt) REVERT: A 266 MET cc_start: 0.7731 (tmm) cc_final: 0.7453 (tmm) REVERT: A 279 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6889 (p90) REVERT: A 329 PHE cc_start: 0.8377 (t80) cc_final: 0.8045 (t80) REVERT: A 454 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8555 (mm) REVERT: A 585 GLU cc_start: 0.8378 (tt0) cc_final: 0.8043 (tt0) REVERT: A 720 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 32 HIS cc_start: 0.7887 (m-70) cc_final: 0.7572 (m-70) REVERT: B 74 PHE cc_start: 0.8297 (m-10) cc_final: 0.7753 (m-80) REVERT: B 154 LYS cc_start: 0.8340 (ptmt) cc_final: 0.8101 (ptpt) outliers start: 34 outliers final: 20 residues processed: 153 average time/residue: 0.0803 time to fit residues: 16.7758 Evaluate side-chains 140 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087384 restraints weight = 13843.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090623 restraints weight = 8449.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092745 restraints weight = 6285.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094054 restraints weight = 5254.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094932 restraints weight = 4706.084| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6889 Z= 0.161 Angle : 0.746 11.790 9376 Z= 0.367 Chirality : 0.044 0.193 1102 Planarity : 0.004 0.040 1177 Dihedral : 6.712 63.832 929 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.48 % Allowed : 23.07 % Favored : 72.46 % 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 aren not related in a simple way. whole: 0.16 (0.30), residues: 843 helix: 1.03 (0.23), residues: 536 sheet: -2.61 (0.71), residues: 40 loop : -1.27 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 40 TYR 0.010 0.001 TYR B 148 PHE 0.016 0.001 PHE A 279 TRP 0.015 0.001 TRP A 144 HIS 0.009 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6889) covalent geometry : angle 0.74581 ( 9376) hydrogen bonds : bond 0.04186 ( 398) hydrogen bonds : angle 4.53566 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8534 (mm-30) REVERT: A 225 MET cc_start: 0.8464 (ttt) cc_final: 0.8240 (ttm) REVERT: A 227 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6179 (tm-30) REVERT: A 266 MET cc_start: 0.7854 (tmm) cc_final: 0.7521 (tmm) REVERT: A 279 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7064 (p90) REVERT: A 329 PHE cc_start: 0.8192 (t80) cc_final: 0.7814 (t80) REVERT: A 368 MET cc_start: 0.8628 (mmm) cc_final: 0.8092 (mtp) REVERT: A 429 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 454 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8589 (mm) REVERT: A 585 GLU cc_start: 0.8490 (tt0) cc_final: 0.8162 (tt0) REVERT: A 720 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: B 32 HIS cc_start: 0.7788 (m-70) cc_final: 0.7431 (m-70) REVERT: B 74 PHE cc_start: 0.8399 (m-10) cc_final: 0.8120 (m-80) outliers start: 33 outliers final: 20 residues processed: 145 average time/residue: 0.0782 time to fit residues: 16.1879 Evaluate side-chains 134 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.0060 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.0070 overall best weight: 0.3812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090334 restraints weight = 26705.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095145 restraints weight = 11499.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096397 restraints weight = 7066.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097221 restraints weight = 5953.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097595 restraints weight = 5558.265| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.7178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6889 Z= 0.130 Angle : 0.718 9.714 9376 Z= 0.349 Chirality : 0.044 0.263 1102 Planarity : 0.004 0.042 1177 Dihedral : 6.565 67.524 928 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.80 % Allowed : 23.07 % Favored : 73.13 % 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 aren not related in a simple way. whole: 0.23 (0.29), residues: 843 helix: 1.15 (0.22), residues: 534 sheet: -2.32 (0.66), residues: 47 loop : -1.38 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.010 0.001 TYR A 544 PHE 0.023 0.001 PHE A 238 TRP 0.013 0.001 TRP A 144 HIS 0.008 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6889) covalent geometry : angle 0.71778 ( 9376) hydrogen bonds : bond 0.03781 ( 398) hydrogen bonds : angle 4.35519 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.296 Fit side-chains REVERT: A 172 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8506 (mm-30) REVERT: A 221 MET cc_start: 0.8881 (ttt) cc_final: 0.8678 (ttm) REVERT: A 225 MET cc_start: 0.8563 (ttt) cc_final: 0.8344 (ttm) REVERT: A 266 MET cc_start: 0.7832 (tmm) cc_final: 0.7477 (tmm) REVERT: A 329 PHE cc_start: 0.8059 (t80) cc_final: 0.7680 (t80) REVERT: A 429 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8330 (mm) REVERT: A 585 GLU cc_start: 0.8437 (tt0) cc_final: 0.8101 (tt0) REVERT: A 634 SER cc_start: 0.9384 (m) cc_final: 0.9030 (p) REVERT: A 710 MET cc_start: 0.8867 (mtt) cc_final: 0.8519 (mmt) REVERT: A 720 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: B 74 PHE cc_start: 0.8354 (m-10) cc_final: 0.8079 (m-80) outliers start: 28 outliers final: 16 residues processed: 139 average time/residue: 0.0756 time to fit residues: 14.8715 Evaluate side-chains 121 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.124804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091744 restraints weight = 16921.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094725 restraints weight = 8793.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096199 restraints weight = 6635.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097110 restraints weight = 5934.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096975 restraints weight = 5392.440| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.7438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6889 Z= 0.135 Angle : 0.723 9.893 9376 Z= 0.350 Chirality : 0.044 0.300 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.358 70.962 923 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.99 % Allowed : 24.15 % Favored : 72.86 % 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 aren not related in a simple way. whole: 0.26 (0.29), residues: 843 helix: 1.18 (0.22), residues: 541 sheet: -2.24 (0.68), residues: 50 loop : -1.47 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 40 TYR 0.012 0.001 TYR A 84 PHE 0.014 0.001 PHE A 279 TRP 0.015 0.001 TRP A 144 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6889) covalent geometry : angle 0.72288 ( 9376) hydrogen bonds : bond 0.03790 ( 398) hydrogen bonds : angle 4.34179 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.272 Fit side-chains REVERT: A 216 THR cc_start: 0.8665 (m) cc_final: 0.8304 (p) REVERT: A 227 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: A 266 MET cc_start: 0.7871 (tmm) cc_final: 0.7461 (tmm) REVERT: A 329 PHE cc_start: 0.8069 (t80) cc_final: 0.7669 (t80) REVERT: A 368 MET cc_start: 0.8505 (mmm) cc_final: 0.8076 (mtp) REVERT: A 429 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8380 (mm) REVERT: A 448 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8282 (tm-30) REVERT: A 585 GLU cc_start: 0.8463 (tt0) cc_final: 0.8142 (tt0) REVERT: A 634 SER cc_start: 0.9403 (m) cc_final: 0.9032 (p) REVERT: B 32 HIS cc_start: 0.7723 (m-70) cc_final: 0.7341 (m-70) REVERT: B 74 PHE cc_start: 0.8386 (m-10) cc_final: 0.8116 (m-80) outliers start: 22 outliers final: 18 residues processed: 127 average time/residue: 0.0742 time to fit residues: 13.2512 Evaluate side-chains 127 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 82 optimal weight: 0.0060 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.0170 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092214 restraints weight = 17132.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096347 restraints weight = 8948.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098326 restraints weight = 5963.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098467 restraints weight = 5380.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098705 restraints weight = 4956.247| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6889 Z= 0.130 Angle : 0.722 10.277 9376 Z= 0.346 Chirality : 0.044 0.301 1102 Planarity : 0.004 0.044 1177 Dihedral : 5.995 74.101 921 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.85 % Allowed : 24.97 % Favored : 72.18 % 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 aren not related in a simple way. whole: 0.33 (0.29), residues: 843 helix: 1.19 (0.22), residues: 545 sheet: -1.94 (0.69), residues: 50 loop : -1.43 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 40 TYR 0.010 0.001 TYR A 544 PHE 0.038 0.001 PHE B 37 TRP 0.013 0.001 TRP A 144 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6889) covalent geometry : angle 0.72220 ( 9376) hydrogen bonds : bond 0.03607 ( 398) hydrogen bonds : angle 4.29853 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.318 Fit side-chains REVERT: A 51 GLU cc_start: 0.8860 (pt0) cc_final: 0.8398 (pt0) REVERT: A 216 THR cc_start: 0.8620 (m) cc_final: 0.8218 (p) REVERT: A 368 MET cc_start: 0.8492 (mmm) cc_final: 0.8067 (mtp) REVERT: A 429 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8309 (mm) REVERT: A 448 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8254 (tm-30) REVERT: A 585 GLU cc_start: 0.8455 (tt0) cc_final: 0.8171 (tt0) REVERT: A 628 ASP cc_start: 0.8542 (m-30) cc_final: 0.8248 (t0) REVERT: A 634 SER cc_start: 0.9396 (m) cc_final: 0.9036 (p) REVERT: A 710 MET cc_start: 0.8750 (mmt) cc_final: 0.8470 (mmt) REVERT: B 32 HIS cc_start: 0.7689 (m-70) cc_final: 0.7318 (m-70) REVERT: B 74 PHE cc_start: 0.8351 (m-10) cc_final: 0.8102 (m-80) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.0759 time to fit residues: 14.4106 Evaluate side-chains 119 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.089901 restraints weight = 24873.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094127 restraints weight = 11383.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095619 restraints weight = 7321.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096328 restraints weight = 6426.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096679 restraints weight = 5969.362| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.7845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6889 Z= 0.138 Angle : 0.739 11.806 9376 Z= 0.353 Chirality : 0.044 0.286 1102 Planarity : 0.004 0.044 1177 Dihedral : 6.027 74.267 921 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.85 % Allowed : 26.05 % Favored : 71.10 % 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 aren not related in a simple way. whole: 0.40 (0.29), residues: 843 helix: 1.22 (0.22), residues: 550 sheet: -1.75 (0.70), residues: 50 loop : -1.45 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.012 0.001 TYR A 203 PHE 0.012 0.001 PHE B 58 TRP 0.015 0.001 TRP A 144 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6889) covalent geometry : angle 0.73926 ( 9376) hydrogen bonds : bond 0.03687 ( 398) hydrogen bonds : angle 4.30692 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.279 Fit side-chains REVERT: A 216 THR cc_start: 0.8732 (m) cc_final: 0.8312 (p) REVERT: A 368 MET cc_start: 0.8457 (mmm) cc_final: 0.8066 (mtp) REVERT: A 429 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 448 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 475 HIS cc_start: 0.8581 (t-90) cc_final: 0.7960 (t-170) REVERT: A 585 GLU cc_start: 0.8335 (tt0) cc_final: 0.7984 (tt0) REVERT: A 628 ASP cc_start: 0.8436 (m-30) cc_final: 0.8190 (t0) REVERT: A 634 SER cc_start: 0.9420 (m) cc_final: 0.9086 (p) REVERT: A 710 MET cc_start: 0.8744 (mmt) cc_final: 0.8413 (mmt) REVERT: B 74 PHE cc_start: 0.8431 (m-10) cc_final: 0.8203 (m-80) outliers start: 21 outliers final: 16 residues processed: 129 average time/residue: 0.0766 time to fit residues: 13.8144 Evaluate side-chains 122 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.088745 restraints weight = 26588.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.093249 restraints weight = 11773.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094122 restraints weight = 7239.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095093 restraints weight = 6473.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095650 restraints weight = 5980.535| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.7987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6889 Z= 0.148 Angle : 0.754 12.180 9376 Z= 0.360 Chirality : 0.044 0.284 1102 Planarity : 0.004 0.044 1177 Dihedral : 6.060 74.780 921 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.44 % Allowed : 26.19 % Favored : 71.37 % 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 aren not related in a simple way. whole: 0.39 (0.29), residues: 843 helix: 1.23 (0.22), residues: 549 sheet: -1.64 (0.69), residues: 50 loop : -1.52 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.019 0.001 TYR A 203 PHE 0.011 0.001 PHE B 58 TRP 0.016 0.001 TRP A 144 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6889) covalent geometry : angle 0.75393 ( 9376) hydrogen bonds : bond 0.03817 ( 398) hydrogen bonds : angle 4.33291 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.319 Fit side-chains REVERT: A 216 THR cc_start: 0.8733 (m) cc_final: 0.8327 (p) REVERT: A 368 MET cc_start: 0.8440 (mmm) cc_final: 0.8095 (mtp) REVERT: A 429 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8411 (mm) REVERT: A 448 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 585 GLU cc_start: 0.8462 (tt0) cc_final: 0.8116 (tt0) REVERT: A 628 ASP cc_start: 0.8541 (m-30) cc_final: 0.8254 (t0) REVERT: A 634 SER cc_start: 0.9419 (m) cc_final: 0.9074 (p) REVERT: A 710 MET cc_start: 0.8756 (mmt) cc_final: 0.8497 (mmt) REVERT: B 74 PHE cc_start: 0.8503 (m-10) cc_final: 0.8215 (m-80) outliers start: 18 outliers final: 15 residues processed: 121 average time/residue: 0.0839 time to fit residues: 14.1993 Evaluate side-chains 120 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 62 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089675 restraints weight = 27064.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.093974 restraints weight = 12906.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095156 restraints weight = 8128.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096091 restraints weight = 6348.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096392 restraints weight = 6020.427| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.8148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6889 Z= 0.144 Angle : 0.747 11.811 9376 Z= 0.358 Chirality : 0.044 0.255 1102 Planarity : 0.004 0.046 1177 Dihedral : 5.972 74.938 919 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.99 % Allowed : 25.51 % Favored : 71.51 % 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 aren not related in a simple way. whole: 0.47 (0.29), residues: 843 helix: 1.23 (0.22), residues: 549 sheet: -1.39 (0.71), residues: 49 loop : -1.37 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.010 0.001 TYR B 148 PHE 0.011 0.001 PHE B 58 TRP 0.016 0.001 TRP A 144 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6889) covalent geometry : angle 0.74730 ( 9376) hydrogen bonds : bond 0.03782 ( 398) hydrogen bonds : angle 4.34168 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1451.99 seconds wall clock time: 25 minutes 46.46 seconds (1546.46 seconds total)