Starting phenix.real_space_refine on Sun Apr 27 17:07:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8scz_40347/04_2025/8scz_40347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8scz_40347/04_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_40347/04_2025/8scz_40347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8scz_40347/04_2025/8scz_40347.map" model { file = "/net/cci-nas-00/data/ceres_data/8scz_40347/04_2025/8scz_40347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8scz_40347/04_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-5669/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: 4.23, per 1000 atoms: 0.66 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: 1.62 Conformation dependent library (CDL) restraints added in 742.8 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: 2.28 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: 2.65 Time building geometry restraints manager: 1.92 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.870 Find NCS groups from input model: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- 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 6668 Z= 0.197 Angle : 0.860 13.246 9289 Z= 0.430 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 Details of bonding type rmsd hydrogen bonds : bond 0.12840 ( 317) hydrogen bonds : angle 5.63470 ( 861) metal coordination : bond 0.01676 ( 4) metal coordination : angle 10.39205 ( 6) covalent geometry : bond 0.00409 ( 6663) covalent geometry : angle 0.81870 ( 9283) Misc. bond : bond 0.00057 ( 1) *********************** 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 : 0.603 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: 0.1583 time to fit residues: 15.7158 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 : 0.611 ------------------------------------------------------------------------------- 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: 3.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 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: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.222070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.179885 restraints weight = 6555.964| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.77 r_work: 0.3948 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6668 Z= 0.132 Angle : 0.538 8.802 9289 Z= 0.263 Chirality : 0.036 0.147 1083 Planarity : 0.004 0.053 962 Dihedral : 17.443 91.633 1614 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.42 % Favored : 94.42 % Rotamer: Outliers : 2.98 % Allowed : 25.04 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.14 (0.32), residues: 627 helix: 0.57 (0.30), residues: 288 sheet: -1.87 (0.56), residues: 88 loop : -1.88 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.004 0.001 HIS A 375 PHE 0.013 0.001 PHE A 856 TYR 0.024 0.002 TYR A 390 ARG 0.005 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 317) hydrogen bonds : angle 4.06750 ( 861) metal coordination : bond 0.00396 ( 4) metal coordination : angle 6.35427 ( 6) covalent geometry : bond 0.00288 ( 6663) covalent geometry : angle 0.51353 ( 9283) Misc. bond : bond 0.00042 ( 1) *********************** 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 85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 1.065 Fit side-chains REVERT: A 469 ASP cc_start: 0.6970 (p0) cc_final: 0.6536 (p0) REVERT: A 569 ASP cc_start: 0.7262 (t0) cc_final: 0.6488 (m-30) REVERT: A 760 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7499 (ptm) outliers start: 17 outliers final: 9 residues processed: 78 average time/residue: 0.2831 time to fit residues: 30.8214 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 : 0.716 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.214437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173223 restraints weight = 6680.875| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.88 r_work: 0.3811 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6668 Z= 0.164 Angle : 0.577 9.568 9289 Z= 0.278 Chirality : 0.038 0.164 1083 Planarity : 0.004 0.051 962 Dihedral : 17.355 95.476 1613 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.38 % Favored : 93.46 % Rotamer: Outliers : 3.85 % Allowed : 23.64 % Favored : 72.50 % 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: -0.62 (0.33), residues: 627 helix: 1.21 (0.31), residues: 284 sheet: -2.05 (0.56), residues: 88 loop : -1.66 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 908 HIS 0.004 0.001 HIS A 281 PHE 0.020 0.002 PHE A 856 TYR 0.023 0.002 TYR A 390 ARG 0.004 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 317) hydrogen bonds : angle 4.03745 ( 861) metal coordination : bond 0.00472 ( 4) metal coordination : angle 6.84185 ( 6) covalent geometry : bond 0.00376 ( 6663) covalent geometry : angle 0.55000 ( 9283) Misc. bond : bond 0.00040 ( 1) *********************** 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 86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.601 Fit side-chains REVERT: A 469 ASP cc_start: 0.7005 (p0) cc_final: 0.6589 (p0) REVERT: A 479 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7856 (mtp) REVERT: A 760 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7618 (ptm) outliers start: 22 outliers final: 15 residues processed: 80 average time/residue: 0.1740 time to fit residues: 18.9758 Evaluate side-chains 72 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.0050 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.215981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175389 restraints weight = 6674.250| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.82 r_work: 0.3805 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6668 Z= 0.129 Angle : 0.529 9.581 9289 Z= 0.254 Chirality : 0.036 0.137 1083 Planarity : 0.004 0.049 962 Dihedral : 17.374 91.887 1613 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.58 % Rotamer: Outliers : 4.20 % Allowed : 25.22 % Favored : 70.58 % 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: -0.23 (0.35), residues: 627 helix: 1.52 (0.31), residues: 284 sheet: -2.10 (0.59), residues: 85 loop : -1.35 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 908 HIS 0.002 0.001 HIS A 691 PHE 0.014 0.001 PHE A 882 TYR 0.019 0.001 TYR A 390 ARG 0.002 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 317) hydrogen bonds : angle 3.92383 ( 861) metal coordination : bond 0.00203 ( 4) metal coordination : angle 6.73342 ( 6) covalent geometry : bond 0.00295 ( 6663) covalent geometry : angle 0.50092 ( 9283) Misc. bond : bond 0.00046 ( 1) *********************** 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 82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6957 (p0) cc_final: 0.6574 (p0) REVERT: A 479 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7577 (mtm) outliers start: 24 outliers final: 15 residues processed: 75 average time/residue: 0.1949 time to fit residues: 21.3828 Evaluate side-chains 70 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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=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: 2.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4413 r_free = 0.4413 target = 0.215034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.173906 restraints weight = 6665.857| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.84 r_work: 0.3777 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6668 Z= 0.133 Angle : 0.542 9.414 9289 Z= 0.257 Chirality : 0.037 0.147 1083 Planarity : 0.003 0.047 962 Dihedral : 17.376 93.092 1613 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.90 % Favored : 93.94 % Rotamer: Outliers : 4.03 % Allowed : 25.39 % Favored : 70.58 % 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: -0.13 (0.35), residues: 627 helix: 1.63 (0.31), residues: 284 sheet: -2.02 (0.59), residues: 83 loop : -1.36 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 908 HIS 0.002 0.001 HIS A 847 PHE 0.011 0.001 PHE A 856 TYR 0.019 0.001 TYR A 390 ARG 0.002 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 317) hydrogen bonds : angle 3.92154 ( 861) metal coordination : bond 0.00236 ( 4) metal coordination : angle 6.71682 ( 6) covalent geometry : bond 0.00306 ( 6663) covalent geometry : angle 0.51421 ( 9283) Misc. bond : bond 0.00042 ( 1) *********************** 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 85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.648 Fit side-chains REVERT: A 469 ASP cc_start: 0.6971 (p0) cc_final: 0.6550 (p0) REVERT: A 479 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7670 (mtm) REVERT: A 859 ARG cc_start: 0.6246 (mtp85) cc_final: 0.5921 (mmt180) outliers start: 23 outliers final: 16 residues processed: 79 average time/residue: 0.1986 time to fit residues: 21.1907 Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 479 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.216020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174072 restraints weight = 6620.552| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.94 r_work: 0.3818 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6668 Z= 0.120 Angle : 0.530 8.808 9289 Z= 0.252 Chirality : 0.037 0.146 1083 Planarity : 0.003 0.048 962 Dihedral : 17.380 91.108 1613 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.85 % Allowed : 25.92 % 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: 0.01 (0.35), residues: 627 helix: 1.78 (0.31), residues: 284 sheet: -2.24 (0.60), residues: 73 loop : -1.28 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 873 HIS 0.003 0.001 HIS A 375 PHE 0.010 0.001 PHE A 882 TYR 0.018 0.001 TYR A 390 ARG 0.002 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 317) hydrogen bonds : angle 3.87802 ( 861) metal coordination : bond 0.00205 ( 4) metal coordination : angle 6.28248 ( 6) covalent geometry : bond 0.00274 ( 6663) covalent geometry : angle 0.50547 ( 9283) Misc. bond : bond 0.00047 ( 1) *********************** 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 82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6882 (p0) cc_final: 0.6492 (p0) REVERT: A 479 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7643 (mtm) REVERT: A 859 ARG cc_start: 0.6158 (mtp85) cc_final: 0.5833 (mmt180) outliers start: 22 outliers final: 17 residues processed: 76 average time/residue: 0.2108 time to fit residues: 22.2908 Evaluate side-chains 73 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.213335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.172115 restraints weight = 6621.826| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.83 r_work: 0.3737 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6668 Z= 0.145 Angle : 0.556 9.163 9289 Z= 0.266 Chirality : 0.037 0.155 1083 Planarity : 0.004 0.047 962 Dihedral : 17.404 94.308 1613 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.38 % Allowed : 25.92 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.35), residues: 627 helix: 1.59 (0.31), residues: 290 sheet: -2.40 (0.60), residues: 76 loop : -1.30 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 908 HIS 0.003 0.001 HIS A 375 PHE 0.012 0.001 PHE A 371 TYR 0.020 0.001 TYR A 390 ARG 0.003 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 317) hydrogen bonds : angle 3.94077 ( 861) metal coordination : bond 0.00304 ( 4) metal coordination : angle 6.35319 ( 6) covalent geometry : bond 0.00334 ( 6663) covalent geometry : angle 0.53193 ( 9283) Misc. bond : bond 0.00046 ( 1) *********************** 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 89 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.636 Fit side-chains REVERT: A 469 ASP cc_start: 0.6813 (p0) cc_final: 0.6471 (p0) REVERT: A 479 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7820 (mtm) REVERT: A 646 TRP cc_start: 0.7350 (t60) cc_final: 0.7135 (t60) REVERT: A 859 ARG cc_start: 0.6117 (mtp85) cc_final: 0.5805 (mmt180) outliers start: 25 outliers final: 18 residues processed: 82 average time/residue: 0.2149 time to fit residues: 24.9650 Evaluate side-chains 76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 520 CYS 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: 5.9990 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** A 710 ASN A 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.214974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174100 restraints weight = 6606.726| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.76 r_work: 0.3808 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6668 Z= 0.128 Angle : 0.552 9.042 9289 Z= 0.266 Chirality : 0.037 0.154 1083 Planarity : 0.003 0.048 962 Dihedral : 17.413 91.534 1613 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.20 % Allowed : 26.80 % 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: -0.04 (0.35), residues: 627 helix: 1.71 (0.31), residues: 285 sheet: -2.30 (0.60), residues: 77 loop : -1.24 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 908 HIS 0.004 0.001 HIS A 375 PHE 0.013 0.001 PHE A 388 TYR 0.018 0.001 TYR A 390 ARG 0.002 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 317) hydrogen bonds : angle 3.89013 ( 861) metal coordination : bond 0.00202 ( 4) metal coordination : angle 6.22142 ( 6) covalent geometry : bond 0.00296 ( 6663) covalent geometry : angle 0.52858 ( 9283) Misc. bond : bond 0.00049 ( 1) *********************** 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 87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6779 (p0) cc_final: 0.6435 (p0) REVERT: A 479 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7717 (mtm) REVERT: A 646 TRP cc_start: 0.7265 (t60) cc_final: 0.7041 (t60) REVERT: A 859 ARG cc_start: 0.6014 (mtp85) cc_final: 0.5708 (mmt180) outliers start: 24 outliers final: 17 residues processed: 80 average time/residue: 0.2740 time to fit residues: 29.9921 Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 419 ASN 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 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 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: 0.0040 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 1 optimal weight: 0.0570 chunk 33 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.4910 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.218470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.177035 restraints weight = 6654.929| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.80 r_work: 0.3869 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6668 Z= 0.103 Angle : 0.515 8.270 9289 Z= 0.249 Chirality : 0.036 0.155 1083 Planarity : 0.003 0.047 962 Dihedral : 17.398 88.243 1613 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.50 % Allowed : 27.85 % 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: 1.93 (0.31), residues: 284 sheet: -2.23 (0.59), residues: 77 loop : -1.13 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 873 HIS 0.004 0.001 HIS A 375 PHE 0.035 0.001 PHE A 388 TYR 0.029 0.001 TYR A 390 ARG 0.002 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 317) hydrogen bonds : angle 3.81858 ( 861) metal coordination : bond 0.00240 ( 4) metal coordination : angle 5.78525 ( 6) covalent geometry : bond 0.00231 ( 6663) covalent geometry : angle 0.49338 ( 9283) Misc. bond : bond 0.00043 ( 1) *********************** 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 86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6911 (p0) cc_final: 0.6590 (p0) REVERT: A 479 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7582 (mtm) REVERT: A 646 TRP cc_start: 0.7201 (t60) cc_final: 0.6736 (t60) REVERT: A 859 ARG cc_start: 0.5976 (mtp85) cc_final: 0.5701 (mmt180) outliers start: 20 outliers final: 13 residues processed: 79 average time/residue: 0.1974 time to fit residues: 21.4076 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 : 0.606 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** A 691 HIS A 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.212728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.171295 restraints weight = 6673.706| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.89 r_work: 0.3785 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6668 Z= 0.165 Angle : 0.598 9.468 9289 Z= 0.287 Chirality : 0.039 0.163 1083 Planarity : 0.004 0.045 962 Dihedral : 17.411 95.005 1613 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.50 % Allowed : 27.67 % Favored : 68.83 % 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: 0.01 (0.35), residues: 627 helix: 1.67 (0.31), residues: 284 sheet: -2.39 (0.60), residues: 79 loop : -1.04 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 908 HIS 0.005 0.001 HIS A 375 PHE 0.015 0.002 PHE A 371 TYR 0.035 0.002 TYR A 390 ARG 0.003 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 317) hydrogen bonds : angle 3.96330 ( 861) metal coordination : bond 0.00361 ( 4) metal coordination : angle 6.46577 ( 6) covalent geometry : bond 0.00386 ( 6663) covalent geometry : angle 0.57565 ( 9283) Misc. bond : bond 0.00046 ( 1) ********************** 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 82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6960 (p0) cc_final: 0.6626 (p0) REVERT: A 479 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7831 (mtm) REVERT: A 646 TRP cc_start: 0.7331 (t60) cc_final: 0.7089 (t60) REVERT: A 859 ARG cc_start: 0.6169 (mtp85) cc_final: 0.5859 (mmt180) outliers start: 20 outliers final: 17 residues processed: 75 average time/residue: 0.1986 time to fit residues: 21.1115 Evaluate side-chains 78 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 525 MET Chi-restraints excluded: chain A residue 574 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 800 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 0.0000 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN A 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.217037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174556 restraints weight = 6803.573| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.97 r_work: 0.3829 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6668 Z= 0.113 Angle : 0.540 8.571 9289 Z= 0.257 Chirality : 0.037 0.171 1083 Planarity : 0.003 0.047 962 Dihedral : 17.418 89.177 1613 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.85 % Allowed : 27.15 % 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: 0.16 (0.35), residues: 627 helix: 1.84 (0.31), residues: 284 sheet: -2.40 (0.57), residues: 82 loop : -0.97 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 873 HIS 0.006 0.001 HIS A 375 PHE 0.009 0.001 PHE A 882 TYR 0.029 0.001 TYR A 390 ARG 0.001 0.000 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 317) hydrogen bonds : angle 3.85128 ( 861) metal coordination : bond 0.00195 ( 4) metal coordination : angle 5.97883 ( 6) covalent geometry : bond 0.00255 ( 6663) covalent geometry : angle 0.51814 ( 9283) Misc. bond : bond 0.00037 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3784.21 seconds wall clock time: 68 minutes 12.77 seconds (4092.77 seconds total)