Starting phenix.real_space_refine on Tue Feb 11 16:29:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8scz_40347/02_2025/8scz_40347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8scz_40347/02_2025/8scz_40347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8scz_40347/02_2025/8scz_40347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8scz_40347/02_2025/8scz_40347.map" model { file = "/net/cci-nas-00/data/ceres_data/8scz_40347/02_2025/8scz_40347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8scz_40347/02_2025/8scz_40347.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 62 5.49 5 S 31 5.16 5 C 3853 2.51 5 N 1092 2.21 5 O 1372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Unusual residues: {'GTP': 1} Classifications: {'RNA': 59, 'undetermined': 1} Modifications used: {'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna3p': 58, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4191 SG CYS A 810 60.315 59.247 80.471 1.00 37.82 S ATOM 4217 SG CYS A 813 62.572 62.668 80.179 1.00 49.69 S ATOM 4630 SG CYS A 864 59.188 62.171 82.238 1.00 46.29 S ATOM 4669 SG CYS A 869 59.417 62.787 78.708 1.00 0.00 S Time building chain proxies: 4.47, per 1000 atoms: 0.70 Number of scatterers: 6411 At special positions: 0 Unit cell: (100.392, 91.848, 111.072, 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) Zn 1 29.99 S 31 16.00 P 62 15.00 O 1372 8.00 N 1092 7.00 C 3853 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 816.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " Number of angles added : 6 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 49.6% alpha, 9.3% beta 29 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.984A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 267 through 284 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.590A pdb=" N ILE A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.883A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.000A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.541A pdb=" N THR A 377 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.876A pdb=" N GLN A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 492 through 497 removed outlier: 4.030A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 removed outlier: 3.869A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 4.074A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.986A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.719A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 771 removed outlier: 4.270A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 removed outlier: 3.513A pdb=" N PHE A 371 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.730A pdb=" N THR A 322 " --> pdb=" O ILE A 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 462 removed outlier: 3.569A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 740 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 3.888A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846 removed outlier: 5.469A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR A 831 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1771 1.34 - 1.46: 1611 1.46 - 1.58: 3116 1.58 - 1.70: 122 1.70 - 1.82: 43 Bond restraints: 6663 Sorted by residual: bond pdb=" C VAL A 332 " pdb=" N PRO A 333 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.32e-02 5.74e+03 4.94e+00 bond pdb=" CB PRO A 626 " pdb=" CG PRO A 626 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.66e+00 bond pdb=" C ILE A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.32e+00 bond pdb=" CB PHE A 388 " pdb=" CG PHE A 388 " ideal model delta sigma weight residual 1.502 1.541 -0.039 2.30e-02 1.89e+03 2.88e+00 bond pdb=" C ILE A 884 " pdb=" N PRO A 885 " ideal model delta sigma weight residual 1.331 1.351 -0.020 1.20e-02 6.94e+03 2.69e+00 ... (remaining 6658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 8965 1.99 - 3.98: 263 3.98 - 5.97: 39 5.97 - 7.96: 12 7.96 - 9.95: 4 Bond angle restraints: 9283 Sorted by residual: angle pdb=" C GLU A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 121.54 130.32 -8.78 1.91e+00 2.74e-01 2.11e+01 angle pdb=" CA PRO A 626 " pdb=" N PRO A 626 " pdb=" CD PRO A 626 " ideal model delta sigma weight residual 112.00 107.07 4.93 1.40e+00 5.10e-01 1.24e+01 angle pdb=" C GLN A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta sigma weight residual 120.33 123.08 -2.75 8.00e-01 1.56e+00 1.18e+01 angle pdb=" CA TYR A 390 " pdb=" CB TYR A 390 " pdb=" CG TYR A 390 " ideal model delta sigma weight residual 113.90 119.94 -6.04 1.80e+00 3.09e-01 1.13e+01 angle pdb=" CA ILE A 300 " pdb=" C ILE A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 120.83 122.88 -2.05 6.10e-01 2.69e+00 1.13e+01 ... (remaining 9278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 3489 18.40 - 36.81: 413 36.81 - 55.21: 141 55.21 - 73.61: 84 73.61 - 92.01: 12 Dihedral angle restraints: 4139 sinusoidal: 2267 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 13.48 91.11 1 2.00e+01 2.50e-03 2.45e+01 dihedral pdb=" CA GLU A 373 " pdb=" C GLU A 373 " pdb=" N CYS A 374 " pdb=" CA CYS A 374 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN A 404 " pdb=" C GLN A 404 " pdb=" N VAL A 405 " pdb=" CA VAL A 405 " ideal model delta harmonic sigma weight residual 180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 810 0.044 - 0.088: 198 0.088 - 0.132: 60 0.132 - 0.175: 12 0.175 - 0.219: 3 Chirality restraints: 1083 Sorted by residual: chirality pdb=" CB ILE A 693 " pdb=" CA ILE A 693 " pdb=" CG1 ILE A 693 " pdb=" CG2 ILE A 693 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL A 877 " pdb=" CA VAL A 877 " pdb=" CG1 VAL A 877 " pdb=" CG2 VAL A 877 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU A 552 " pdb=" CB LEU A 552 " pdb=" CD1 LEU A 552 " pdb=" CD2 LEU A 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 1080 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 342 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASP A 342 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP A 342 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE A 343 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 800 " -0.061 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO A 801 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 801 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 801 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 390 " 0.016 2.00e-02 2.50e+03 2.14e-02 9.17e+00 pdb=" CG TYR A 390 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 390 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 390 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 390 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 390 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 390 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 390 " 0.000 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 21 2.45 - 3.06: 3585 3.06 - 3.67: 10435 3.67 - 4.29: 14899 4.29 - 4.90: 23675 Nonbonded interactions: 52615 Sorted by model distance: nonbonded pdb=" OH TYR A 246 " pdb=" CD1 LEU A 449 " model vdw 1.836 3.460 nonbonded pdb=" CE1 PHE A 460 " pdb=" CD2 LEU A 740 " model vdw 2.268 3.760 nonbonded pdb=" O GLN A 457 " pdb=" CD2 PHE A 459 " model vdw 2.285 3.340 nonbonded pdb=" O GLN A 511 " pdb=" OG1 THR A 515 " model vdw 2.304 3.040 nonbonded pdb=" O GLU A 583 " pdb=" OG1 THR A 587 " model vdw 2.315 3.040 ... (remaining 52610 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 : 0.004 0.108 6663 Z= 0.273 Angle : 0.819 9.946 9283 Z= 0.427 Chirality : 0.044 0.219 1083 Planarity : 0.006 0.094 962 Dihedral : 19.405 92.015 2919 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.22 % Favored : 93.62 % Rotamer: Outliers : 0.35 % Allowed : 27.32 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.29), residues: 627 helix: -0.88 (0.27), residues: 279 sheet: -2.03 (0.58), residues: 74 loop : -1.81 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 908 HIS 0.005 0.001 HIS A 375 PHE 0.032 0.002 PHE A 388 TYR 0.052 0.003 TYR A 390 ARG 0.008 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.641 Fit side-chains REVERT: A 279 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 469 ASP cc_start: 0.6996 (p0) cc_final: 0.6607 (p0) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.1625 time to fit residues: 15.9997 Evaluate side-chains 58 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 800 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 chunk 62 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.223138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.181209 restraints weight = 6540.257| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.74 r_work: 0.3974 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6663 Z= 0.175 Angle : 0.511 6.743 9283 Z= 0.259 Chirality : 0.036 0.142 1083 Planarity : 0.004 0.053 962 Dihedral : 17.441 90.782 1614 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.58 % Rotamer: Outliers : 2.98 % Allowed : 25.39 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.32), residues: 627 helix: 0.54 (0.29), residues: 288 sheet: -1.85 (0.56), residues: 88 loop : -1.87 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 771 HIS 0.004 0.001 HIS A 375 PHE 0.011 0.001 PHE A 856 TYR 0.024 0.002 TYR A 390 ARG 0.005 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.646 Fit side-chains REVERT: A 469 ASP cc_start: 0.6983 (p0) cc_final: 0.6546 (p0) REVERT: A 569 ASP cc_start: 0.7285 (t0) cc_final: 0.6518 (m-30) REVERT: A 760 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7505 (ptm) outliers start: 17 outliers final: 9 residues processed: 76 average time/residue: 0.1591 time to fit residues: 17.0298 Evaluate side-chains 69 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.212631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171139 restraints weight = 6681.642| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.87 r_work: 0.3754 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6663 Z= 0.286 Angle : 0.580 7.273 9283 Z= 0.291 Chirality : 0.039 0.168 1083 Planarity : 0.004 0.050 962 Dihedral : 17.384 97.075 1613 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.70 % Favored : 93.14 % Rotamer: Outliers : 3.68 % Allowed : 23.64 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.33), residues: 627 helix: 1.11 (0.31), residues: 284 sheet: -2.18 (0.54), residues: 90 loop : -1.64 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 908 HIS 0.004 0.001 HIS A 281 PHE 0.022 0.002 PHE A 856 TYR 0.024 0.002 TYR A 390 ARG 0.004 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.620 Fit side-chains REVERT: A 469 ASP cc_start: 0.7049 (p0) cc_final: 0.6628 (p0) REVERT: A 479 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7942 (mtp) REVERT: A 760 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7640 (ptm) outliers start: 21 outliers final: 14 residues processed: 79 average time/residue: 0.1976 time to fit residues: 20.8063 Evaluate side-chains 69 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.216962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.176738 restraints weight = 6669.516| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.81 r_work: 0.3823 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6663 Z= 0.175 Angle : 0.494 6.641 9283 Z= 0.248 Chirality : 0.036 0.133 1083 Planarity : 0.003 0.049 962 Dihedral : 17.387 90.772 1613 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 3.50 % Allowed : 24.87 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.35), residues: 627 helix: 1.54 (0.31), residues: 284 sheet: -1.96 (0.60), residues: 83 loop : -1.40 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 873 HIS 0.002 0.000 HIS A 691 PHE 0.009 0.001 PHE A 856 TYR 0.018 0.001 TYR A 390 ARG 0.002 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 261 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7837 (mm) REVERT: A 469 ASP cc_start: 0.6923 (p0) cc_final: 0.6535 (p0) REVERT: A 479 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7530 (mtm) outliers start: 20 outliers final: 13 residues processed: 71 average time/residue: 0.1550 time to fit residues: 15.6632 Evaluate side-chains 69 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.209797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.167763 restraints weight = 6689.028| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.88 r_work: 0.3736 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6663 Z= 0.312 Angle : 0.597 8.268 9283 Z= 0.296 Chirality : 0.039 0.172 1083 Planarity : 0.004 0.047 962 Dihedral : 17.455 98.181 1613 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.02 % Favored : 92.82 % Rotamer: Outliers : 4.38 % Allowed : 24.69 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.34), residues: 627 helix: 1.32 (0.31), residues: 284 sheet: -2.37 (0.57), residues: 85 loop : -1.44 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 908 HIS 0.004 0.001 HIS A 847 PHE 0.018 0.002 PHE A 856 TYR 0.021 0.002 TYR A 390 ARG 0.004 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.596 Fit side-chains REVERT: A 469 ASP cc_start: 0.6989 (p0) cc_final: 0.6596 (p0) REVERT: A 479 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7885 (mtm) REVERT: A 784 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7314 (pt0) outliers start: 25 outliers final: 18 residues processed: 77 average time/residue: 0.1644 time to fit residues: 17.7114 Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.0370 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.217354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176216 restraints weight = 6606.020| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.98 r_work: 0.3824 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6663 Z= 0.151 Angle : 0.497 8.178 9283 Z= 0.247 Chirality : 0.036 0.143 1083 Planarity : 0.003 0.047 962 Dihedral : 17.445 87.496 1613 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.33 % Allowed : 26.44 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.35), residues: 627 helix: 1.69 (0.31), residues: 291 sheet: -2.11 (0.62), residues: 74 loop : -1.37 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 771 HIS 0.002 0.000 HIS A 375 PHE 0.013 0.001 PHE A 882 TYR 0.017 0.001 TYR A 390 ARG 0.002 0.000 ARG A 791 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6794 (p0) cc_final: 0.6416 (p0) REVERT: A 479 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7830 (mtm) REVERT: A 859 ARG cc_start: 0.6180 (mtp85) cc_final: 0.5854 (mmt180) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.2017 time to fit residues: 21.0571 Evaluate side-chains 69 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.206305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163551 restraints weight = 6681.492| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.83 r_work: 0.3710 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 6663 Z= 0.397 Angle : 0.657 7.460 9283 Z= 0.328 Chirality : 0.041 0.181 1083 Planarity : 0.004 0.044 962 Dihedral : 17.565 99.453 1613 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.73 % Allowed : 26.62 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.34), residues: 627 helix: 1.11 (0.31), residues: 290 sheet: -2.38 (0.64), residues: 71 loop : -1.60 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 908 HIS 0.005 0.001 HIS A 871 PHE 0.022 0.002 PHE A 776 TYR 0.020 0.002 TYR A 390 ARG 0.005 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.647 Fit side-chains REVERT: A 469 ASP cc_start: 0.6983 (p0) cc_final: 0.6588 (p0) REVERT: A 479 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8049 (mtm) REVERT: A 523 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7390 (m-10) outliers start: 27 outliers final: 18 residues processed: 77 average time/residue: 0.1577 time to fit residues: 16.9877 Evaluate side-chains 73 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 59 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.215166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.172950 restraints weight = 6633.181| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.74 r_work: 0.3894 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6663 Z= 0.163 Angle : 0.535 7.012 9283 Z= 0.265 Chirality : 0.037 0.146 1083 Planarity : 0.004 0.047 962 Dihedral : 17.529 88.487 1613 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.03 % Allowed : 26.97 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.34), residues: 627 helix: 1.41 (0.31), residues: 292 sheet: -2.58 (0.55), residues: 84 loop : -1.39 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 771 HIS 0.002 0.001 HIS A 375 PHE 0.012 0.001 PHE A 882 TYR 0.018 0.001 TYR A 390 ARG 0.002 0.000 ARG A 791 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6836 (p0) cc_final: 0.6485 (p0) REVERT: A 479 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7794 (mtm) REVERT: A 646 TRP cc_start: 0.7449 (t60) cc_final: 0.7221 (t60) REVERT: A 859 ARG cc_start: 0.6097 (mtp85) cc_final: 0.5814 (mmt180) outliers start: 23 outliers final: 15 residues processed: 78 average time/residue: 0.1832 time to fit residues: 19.7193 Evaluate side-chains 71 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 chunk 67 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 0.0010 chunk 33 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.0670 chunk 61 optimal weight: 0.8980 overall best weight: 0.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.221526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.180632 restraints weight = 6686.466| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.71 r_work: 0.3906 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6663 Z= 0.152 Angle : 0.511 9.344 9283 Z= 0.254 Chirality : 0.036 0.172 1083 Planarity : 0.004 0.056 962 Dihedral : 17.441 86.006 1613 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.98 % Allowed : 29.07 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.35), residues: 627 helix: 1.83 (0.31), residues: 286 sheet: -2.05 (0.67), residues: 66 loop : -1.23 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 771 HIS 0.007 0.001 HIS A 281 PHE 0.015 0.001 PHE A 388 TYR 0.027 0.001 TYR A 390 ARG 0.003 0.000 ARG A 791 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6860 (p0) cc_final: 0.6542 (p0) REVERT: A 479 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7517 (mtm) REVERT: A 646 TRP cc_start: 0.7210 (t60) cc_final: 0.6720 (t60) REVERT: A 859 ARG cc_start: 0.5918 (mtp85) cc_final: 0.5684 (mmt180) outliers start: 17 outliers final: 12 residues processed: 78 average time/residue: 0.1805 time to fit residues: 19.2644 Evaluate side-chains 73 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.217791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.175743 restraints weight = 6669.106| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.70 r_work: 0.3839 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6663 Z= 0.183 Angle : 0.520 7.305 9283 Z= 0.257 Chirality : 0.037 0.158 1083 Planarity : 0.003 0.046 962 Dihedral : 17.385 90.305 1613 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.63 % Allowed : 29.07 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.35), residues: 627 helix: 1.78 (0.31), residues: 285 sheet: -2.49 (0.57), residues: 81 loop : -1.07 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 771 HIS 0.005 0.001 HIS A 375 PHE 0.010 0.001 PHE A 882 TYR 0.030 0.001 TYR A 390 ARG 0.002 0.000 ARG A 546 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6855 (p0) cc_final: 0.6546 (p0) REVERT: A 479 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7543 (mtm) REVERT: A 646 TRP cc_start: 0.7209 (t60) cc_final: 0.6734 (t60) REVERT: A 859 ARG cc_start: 0.6072 (mtp85) cc_final: 0.5784 (mmt180) REVERT: A 883 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7058 (mm-30) outliers start: 15 outliers final: 13 residues processed: 69 average time/residue: 0.1926 time to fit residues: 17.7777 Evaluate side-chains 72 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 0.0170 chunk 2 optimal weight: 0.0570 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 overall best weight: 0.2534 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.222667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.181809 restraints weight = 6795.771| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.79 r_work: 0.3899 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6663 Z= 0.140 Angle : 0.510 7.879 9283 Z= 0.249 Chirality : 0.037 0.169 1083 Planarity : 0.003 0.046 962 Dihedral : 17.360 84.522 1613 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.63 % Allowed : 28.72 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.35), residues: 627 helix: 1.88 (0.31), residues: 286 sheet: -2.28 (0.59), residues: 76 loop : -1.08 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 771 HIS 0.004 0.001 HIS A 375 PHE 0.012 0.001 PHE A 882 TYR 0.025 0.001 TYR A 390 ARG 0.002 0.000 ARG A 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2998.15 seconds wall clock time: 54 minutes 13.23 seconds (3253.23 seconds total)