Starting phenix.real_space_refine on Tue Mar 3 14:11:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7v_72666/03_2026/9y7v_72666.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7v_72666/03_2026/9y7v_72666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y7v_72666/03_2026/9y7v_72666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7v_72666/03_2026/9y7v_72666.map" model { file = "/net/cci-nas-00/data/ceres_data/9y7v_72666/03_2026/9y7v_72666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7v_72666/03_2026/9y7v_72666.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 12 5.16 5 C 3498 2.51 5 N 1008 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5625 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "E" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "F" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.33, per 1000 atoms: 0.24 Number of scatterers: 5625 At special positions: 0 Unit cell: (90.16, 86.48, 71.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 9 15.00 O 1098 8.00 N 1008 7.00 C 3498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 309.9 milliseconds 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 45.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'D' and resid 322 through 338 Processing helix chain 'D' and resid 350 through 369 removed outlier: 5.823A pdb=" N ALA D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.699A pdb=" N PHE D 378 " --> pdb=" O PHE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 432 Processing helix chain 'D' and resid 433 through 451 Processing helix chain 'D' and resid 454 through 459 removed outlier: 3.730A pdb=" N LEU D 458 " --> pdb=" O PRO D 455 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER D 459 " --> pdb=" O ASP D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 472 Processing helix chain 'D' and resid 527 through 545 removed outlier: 3.781A pdb=" N GLY D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 552 Processing helix chain 'E' and resid 322 through 338 removed outlier: 3.503A pdb=" N ARG E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 369 removed outlier: 5.612A pdb=" N ALA E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 389 removed outlier: 3.815A pdb=" N PHE E 378 " --> pdb=" O PHE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 433 through 451 Processing helix chain 'E' and resid 454 through 459 removed outlier: 3.531A pdb=" N LEU E 458 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 459 " --> pdb=" O ASP E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 472 Processing helix chain 'E' and resid 527 through 545 removed outlier: 3.716A pdb=" N GLY E 545 " --> pdb=" O ARG E 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 338 Processing helix chain 'F' and resid 350 through 369 removed outlier: 5.675A pdb=" N ALA F 362 " --> pdb=" O ALA F 358 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA F 363 " --> pdb=" O ARG F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 389 removed outlier: 3.731A pdb=" N PHE F 378 " --> pdb=" O PHE F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 432 Processing helix chain 'F' and resid 433 through 451 Processing helix chain 'F' and resid 454 through 459 removed outlier: 3.509A pdb=" N LEU F 458 " --> pdb=" O PRO F 455 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER F 459 " --> pdb=" O ASP F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 472 Processing helix chain 'F' and resid 527 through 545 removed outlier: 3.723A pdb=" N GLY F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 552 Processing sheet with id=AA1, first strand: chain 'D' and resid 318 through 320 removed outlier: 3.715A pdb=" N GLN D 319 " --> pdb=" O ILE E 403 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 349 removed outlier: 3.800A pdb=" N CYS D 515 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 510 " --> pdb=" O ARG D 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 394 through 397 removed outlier: 3.648A pdb=" N GLN F 319 " --> pdb=" O ILE D 403 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 425 through 427 removed outlier: 6.454A pdb=" N THR D 464 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N THR D 490 " --> pdb=" O THR D 464 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 466 " --> pdb=" O THR D 490 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 415 through 416 Processing sheet with id=AA6, first strand: chain 'E' and resid 318 through 319 removed outlier: 3.878A pdb=" N GLN E 319 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE F 403 " --> pdb=" O GLN E 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 348 through 349 removed outlier: 3.512A pdb=" N VAL E 348 " --> pdb=" O CYS E 515 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS E 515 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY E 510 " --> pdb=" O ARG E 498 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 494 " --> pdb=" O VAL E 514 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.565A pdb=" N ILE E 465 " --> pdb=" O GLY E 412 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR E 464 " --> pdb=" O LEU E 488 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR E 490 " --> pdb=" O THR E 464 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR E 466 " --> pdb=" O THR E 490 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR E 520 " --> pdb=" O MET E 487 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AB1, first strand: chain 'F' and resid 347 through 349 removed outlier: 3.528A pdb=" N VAL F 348 " --> pdb=" O CYS F 515 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS F 515 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY F 510 " --> pdb=" O ARG F 498 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 494 " --> pdb=" O VAL F 514 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 425 through 427 removed outlier: 3.573A pdb=" N ILE F 465 " --> pdb=" O GLY F 412 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR F 464 " --> pdb=" O LEU F 488 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR F 490 " --> pdb=" O THR F 464 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR F 466 " --> pdb=" O THR F 490 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR F 520 " --> pdb=" O MET F 487 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 415 through 417 272 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.53 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: 1899 1.34 - 1.46: 1009 1.46 - 1.58: 2775 1.58 - 1.70: 17 1.70 - 1.82: 18 Bond restraints: 5718 Sorted by residual: bond pdb=" CCP COA E 601 " pdb=" O6A COA E 601 " ideal model delta sigma weight residual 1.431 1.342 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CCP COA F 601 " pdb=" O6A COA F 601 " ideal model delta sigma weight residual 1.431 1.348 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CCP COA D 601 " pdb=" O6A COA D 601 " ideal model delta sigma weight residual 1.431 1.354 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C9P COA D 601 " pdb=" N8P COA D 601 " ideal model delta sigma weight residual 1.340 1.416 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C9P COA F 601 " pdb=" N8P COA F 601 " ideal model delta sigma weight residual 1.340 1.413 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 5713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 7637 2.62 - 5.24: 88 5.24 - 7.86: 37 7.86 - 10.48: 11 10.48 - 13.10: 3 Bond angle restraints: 7776 Sorted by residual: angle pdb=" O1A COA D 601 " pdb=" P1A COA D 601 " pdb=" O3A COA D 601 " ideal model delta sigma weight residual 110.50 97.40 13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" O1A COA E 601 " pdb=" P1A COA E 601 " pdb=" O3A COA E 601 " ideal model delta sigma weight residual 110.50 97.47 13.03 3.00e+00 1.11e-01 1.89e+01 angle pdb=" O1A COA F 601 " pdb=" P1A COA F 601 " pdb=" O3A COA F 601 " ideal model delta sigma weight residual 110.50 97.50 13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" O4A COA F 601 " pdb=" P2A COA F 601 " pdb=" O6A COA F 601 " ideal model delta sigma weight residual 110.27 100.69 9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" O4A COA E 601 " pdb=" P2A COA E 601 " pdb=" O6A COA E 601 " ideal model delta sigma weight residual 110.27 100.71 9.56 3.00e+00 1.11e-01 1.02e+01 ... (remaining 7771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3170 17.52 - 35.04: 286 35.04 - 52.55: 64 52.55 - 70.07: 22 70.07 - 87.59: 1 Dihedral angle restraints: 3543 sinusoidal: 1482 harmonic: 2061 Sorted by residual: dihedral pdb=" CA PHE F 475 " pdb=" C PHE F 475 " pdb=" N ASP F 476 " pdb=" CA ASP F 476 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE D 475 " pdb=" C PHE D 475 " pdb=" N ASP D 476 " pdb=" CA ASP D 476 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE E 475 " pdb=" C PHE E 475 " pdb=" N ASP E 476 " pdb=" CA ASP E 476 " ideal model delta harmonic sigma weight residual -180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 832 0.079 - 0.158: 62 0.158 - 0.237: 3 0.237 - 0.316: 1 0.316 - 0.395: 5 Chirality restraints: 903 Sorted by residual: chirality pdb=" C2B COA E 601 " pdb=" C1B COA E 601 " pdb=" C3B COA E 601 " pdb=" O2B COA E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C2B COA D 601 " pdb=" C1B COA D 601 " pdb=" C3B COA D 601 " pdb=" O2B COA D 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C2B COA F 601 " pdb=" C1B COA F 601 " pdb=" C3B COA F 601 " pdb=" O2B COA F 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 900 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 496 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO F 497 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO F 497 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 497 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 496 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO E 497 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 497 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 497 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 496 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO D 497 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 497 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 497 " 0.019 5.00e-02 4.00e+02 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 633 2.74 - 3.28: 5230 3.28 - 3.82: 8817 3.82 - 4.36: 10058 4.36 - 4.90: 17898 Nonbonded interactions: 42636 Sorted by model distance: nonbonded pdb=" NH2 ARG D 496 " pdb=" OE1 GLU E 347 " model vdw 2.204 3.120 nonbonded pdb=" OG1 THR D 464 " pdb=" OE1 GLN D 484 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR E 464 " pdb=" OE1 GLN E 484 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR F 464 " pdb=" OE1 GLN F 484 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP D 476 " pdb=" N THR D 477 " model vdw 2.233 3.120 ... (remaining 42631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.240 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.006 0.089 5718 Z= 0.319 Angle : 0.885 13.101 7776 Z= 0.395 Chirality : 0.050 0.395 903 Planarity : 0.004 0.043 1002 Dihedral : 14.316 87.587 2217 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.32), residues: 717 helix: 2.53 (0.30), residues: 282 sheet: -0.26 (0.40), residues: 150 loop : 0.47 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 449 TYR 0.012 0.001 TYR E 405 PHE 0.009 0.002 PHE E 475 HIS 0.011 0.002 HIS E 523 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 5718) covalent geometry : angle 0.88457 ( 7776) hydrogen bonds : bond 0.18168 ( 272) hydrogen bonds : angle 6.60431 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 415 VAL cc_start: 0.9166 (t) cc_final: 0.8956 (p) REVERT: D 422 LEU cc_start: 0.8705 (mt) cc_final: 0.8452 (mp) REVERT: E 341 GLN cc_start: 0.7781 (mt0) cc_final: 0.7458 (mt0) REVERT: E 396 TYR cc_start: 0.8568 (t80) cc_final: 0.7844 (t80) REVERT: E 487 MET cc_start: 0.8053 (ttm) cc_final: 0.7641 (ttm) REVERT: F 341 GLN cc_start: 0.7868 (mt0) cc_final: 0.7525 (mt0) REVERT: F 364 PHE cc_start: 0.7676 (t80) cc_final: 0.7420 (t80) REVERT: F 422 LEU cc_start: 0.8854 (mt) cc_final: 0.8551 (mp) REVERT: F 487 MET cc_start: 0.8198 (ttt) cc_final: 0.7921 (ttm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.0924 time to fit residues: 29.5094 Evaluate side-chains 101 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 523 HIS E 346 HIS ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096761 restraints weight = 9841.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099746 restraints weight = 6610.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101603 restraints weight = 5291.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102327 restraints weight = 4656.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103309 restraints weight = 4381.944| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 5718 Z= 0.279 Angle : 0.684 6.897 7776 Z= 0.355 Chirality : 0.044 0.159 903 Planarity : 0.005 0.043 1002 Dihedral : 11.029 59.743 966 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.31), residues: 717 helix: 1.70 (0.29), residues: 285 sheet: -0.37 (0.42), residues: 156 loop : 0.46 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 524 TYR 0.013 0.003 TYR D 521 PHE 0.016 0.002 PHE F 534 HIS 0.005 0.001 HIS D 523 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 5718) covalent geometry : angle 0.68403 ( 7776) hydrogen bonds : bond 0.05491 ( 272) hydrogen bonds : angle 5.26647 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 380 LYS cc_start: 0.9072 (tppt) cc_final: 0.8820 (tttt) REVERT: D 393 ASN cc_start: 0.9203 (t0) cc_final: 0.8759 (t0) REVERT: D 396 TYR cc_start: 0.8617 (t80) cc_final: 0.8363 (t80) REVERT: D 406 TYR cc_start: 0.7658 (m-80) cc_final: 0.6929 (m-10) REVERT: D 415 VAL cc_start: 0.9121 (t) cc_final: 0.8887 (p) REVERT: D 487 MET cc_start: 0.7528 (ttm) cc_final: 0.7147 (mtp) REVERT: E 361 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8389 (ptpt) REVERT: E 393 ASN cc_start: 0.9273 (t0) cc_final: 0.9013 (t0) REVERT: E 401 LYS cc_start: 0.9210 (mptt) cc_final: 0.8982 (mmtt) REVERT: E 406 TYR cc_start: 0.8008 (m-80) cc_final: 0.7429 (m-10) REVERT: E 471 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8269 (mp10) REVERT: E 487 MET cc_start: 0.8097 (ttm) cc_final: 0.7872 (mtp) REVERT: F 335 SER cc_start: 0.9329 (m) cc_final: 0.9110 (p) REVERT: F 393 ASN cc_start: 0.9180 (t0) cc_final: 0.8856 (t0) REVERT: F 513 SER cc_start: 0.9398 (m) cc_final: 0.9022 (p) REVERT: F 521 TYR cc_start: 0.8754 (p90) cc_final: 0.8438 (p90) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.0827 time to fit residues: 13.9540 Evaluate side-chains 81 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN D 346 HIS F 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096758 restraints weight = 9605.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099723 restraints weight = 6418.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101647 restraints weight = 5083.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102496 restraints weight = 4443.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103268 restraints weight = 4142.558| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 5718 Z= 0.248 Angle : 0.631 6.418 7776 Z= 0.327 Chirality : 0.041 0.146 903 Planarity : 0.005 0.044 1002 Dihedral : 10.241 53.833 966 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.32), residues: 717 helix: 1.63 (0.30), residues: 288 sheet: -0.21 (0.43), residues: 150 loop : 0.24 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 439 TYR 0.022 0.002 TYR E 405 PHE 0.015 0.002 PHE F 534 HIS 0.005 0.001 HIS F 540 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 5718) covalent geometry : angle 0.63096 ( 7776) hydrogen bonds : bond 0.04994 ( 272) hydrogen bonds : angle 4.82985 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 393 ASN cc_start: 0.9210 (t0) cc_final: 0.8671 (t0) REVERT: D 396 TYR cc_start: 0.8588 (t80) cc_final: 0.8361 (t80) REVERT: D 406 TYR cc_start: 0.7659 (m-80) cc_final: 0.6466 (m-10) REVERT: D 444 ILE cc_start: 0.9440 (mm) cc_final: 0.8936 (tt) REVERT: D 487 MET cc_start: 0.7515 (ttm) cc_final: 0.7140 (mtp) REVERT: E 393 ASN cc_start: 0.9273 (t0) cc_final: 0.8451 (t0) REVERT: E 401 LYS cc_start: 0.9199 (mptt) cc_final: 0.8877 (mptt) REVERT: E 406 TYR cc_start: 0.7933 (m-80) cc_final: 0.6051 (m-10) REVERT: E 471 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8473 (mp10) REVERT: F 341 GLN cc_start: 0.8397 (mt0) cc_final: 0.8073 (mt0) REVERT: F 391 ASN cc_start: 0.8069 (p0) cc_final: 0.7526 (m-40) REVERT: F 393 ASN cc_start: 0.9158 (t0) cc_final: 0.8842 (t0) REVERT: F 487 MET cc_start: 0.8302 (ttm) cc_final: 0.7853 (mtp) REVERT: F 521 TYR cc_start: 0.8756 (p90) cc_final: 0.8515 (p90) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0897 time to fit residues: 12.3335 Evaluate side-chains 81 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN D 427 HIS E 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102947 restraints weight = 9501.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104704 restraints weight = 8085.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105877 restraints weight = 5789.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106018 restraints weight = 5455.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107229 restraints weight = 4896.019| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5718 Z= 0.140 Angle : 0.557 5.793 7776 Z= 0.288 Chirality : 0.039 0.127 903 Planarity : 0.004 0.046 1002 Dihedral : 9.664 52.132 966 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.32), residues: 717 helix: 2.00 (0.30), residues: 285 sheet: -0.42 (0.38), residues: 189 loop : 0.84 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 325 TYR 0.020 0.002 TYR E 405 PHE 0.019 0.001 PHE F 534 HIS 0.003 0.001 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5718) covalent geometry : angle 0.55669 ( 7776) hydrogen bonds : bond 0.04154 ( 272) hydrogen bonds : angle 4.55720 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 MET cc_start: 0.8686 (mmm) cc_final: 0.8217 (mmm) REVERT: D 361 LYS cc_start: 0.9016 (ptpp) cc_final: 0.8614 (ptpt) REVERT: D 444 ILE cc_start: 0.9386 (mm) cc_final: 0.8870 (tt) REVERT: E 391 ASN cc_start: 0.7955 (p0) cc_final: 0.7432 (t0) REVERT: E 393 ASN cc_start: 0.9168 (t0) cc_final: 0.8868 (t0) REVERT: E 401 LYS cc_start: 0.9193 (mptt) cc_final: 0.8959 (mptt) REVERT: E 471 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8443 (mp10) REVERT: E 487 MET cc_start: 0.8104 (ttp) cc_final: 0.7456 (mtp) REVERT: F 391 ASN cc_start: 0.7922 (p0) cc_final: 0.7329 (m-40) REVERT: F 393 ASN cc_start: 0.9013 (t0) cc_final: 0.8650 (t0) REVERT: F 406 TYR cc_start: 0.7816 (m-80) cc_final: 0.7145 (m-10) REVERT: F 487 MET cc_start: 0.8159 (ttm) cc_final: 0.7904 (mtp) REVERT: F 521 TYR cc_start: 0.8646 (p90) cc_final: 0.8444 (p90) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0996 time to fit residues: 13.6949 Evaluate side-chains 80 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.0980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 GLN E 344 GLN E 346 HIS E 467 ASN F 467 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.096920 restraints weight = 9745.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099892 restraints weight = 6397.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101803 restraints weight = 5012.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103039 restraints weight = 4394.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103580 restraints weight = 4041.848| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5718 Z= 0.159 Angle : 0.565 5.442 7776 Z= 0.289 Chirality : 0.040 0.127 903 Planarity : 0.004 0.039 1002 Dihedral : 9.127 47.890 966 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.18 % Allowed : 2.12 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.32), residues: 717 helix: 2.17 (0.30), residues: 285 sheet: -0.46 (0.42), residues: 150 loop : 0.37 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 524 TYR 0.015 0.001 TYR E 405 PHE 0.015 0.002 PHE F 364 HIS 0.003 0.001 HIS E 427 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5718) covalent geometry : angle 0.56507 ( 7776) hydrogen bonds : bond 0.04024 ( 272) hydrogen bonds : angle 4.35239 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 MET cc_start: 0.8712 (mmm) cc_final: 0.8315 (mmm) REVERT: D 391 ASN cc_start: 0.8136 (p0) cc_final: 0.7499 (t0) REVERT: D 397 ASN cc_start: 0.8987 (t0) cc_final: 0.8661 (t0) REVERT: D 444 ILE cc_start: 0.9475 (mm) cc_final: 0.9009 (tt) REVERT: E 391 ASN cc_start: 0.8102 (p0) cc_final: 0.7335 (t0) REVERT: E 393 ASN cc_start: 0.9316 (t0) cc_final: 0.8981 (t0) REVERT: E 401 LYS cc_start: 0.9225 (mptt) cc_final: 0.8995 (mptt) REVERT: E 471 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8518 (mm-40) REVERT: F 391 ASN cc_start: 0.8036 (p0) cc_final: 0.7220 (t0) REVERT: F 393 ASN cc_start: 0.9114 (t0) cc_final: 0.8735 (t0) REVERT: F 406 TYR cc_start: 0.7760 (m-80) cc_final: 0.7118 (m-10) REVERT: F 487 MET cc_start: 0.8345 (ttm) cc_final: 0.7963 (mtp) REVERT: F 521 TYR cc_start: 0.8744 (p90) cc_final: 0.8481 (p90) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.0867 time to fit residues: 11.6571 Evaluate side-chains 87 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN D 427 HIS E 341 GLN F 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096078 restraints weight = 9637.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099028 restraints weight = 6387.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100889 restraints weight = 5031.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102148 restraints weight = 4394.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102680 restraints weight = 4054.471| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5718 Z= 0.163 Angle : 0.568 5.532 7776 Z= 0.295 Chirality : 0.039 0.134 903 Planarity : 0.004 0.039 1002 Dihedral : 8.521 46.244 966 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.32), residues: 717 helix: 2.24 (0.30), residues: 285 sheet: 0.12 (0.41), residues: 147 loop : -0.02 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 315 TYR 0.011 0.001 TYR E 405 PHE 0.018 0.002 PHE F 364 HIS 0.010 0.001 HIS E 346 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5718) covalent geometry : angle 0.56769 ( 7776) hydrogen bonds : bond 0.03955 ( 272) hydrogen bonds : angle 4.46113 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 MET cc_start: 0.8748 (mmm) cc_final: 0.8322 (mmm) REVERT: D 397 ASN cc_start: 0.8828 (t0) cc_final: 0.8510 (t0) REVERT: D 444 ILE cc_start: 0.9514 (mm) cc_final: 0.9066 (tt) REVERT: E 391 ASN cc_start: 0.8155 (p0) cc_final: 0.7424 (t0) REVERT: E 393 ASN cc_start: 0.9350 (t0) cc_final: 0.9071 (t0) REVERT: E 397 ASN cc_start: 0.9206 (t0) cc_final: 0.8831 (t0) REVERT: E 401 LYS cc_start: 0.9230 (mptt) cc_final: 0.8955 (mptt) REVERT: E 471 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8468 (mp10) REVERT: E 487 MET cc_start: 0.8463 (ttp) cc_final: 0.7668 (mtp) REVERT: F 333 ARG cc_start: 0.8710 (ttp-170) cc_final: 0.8458 (tmt-80) REVERT: F 391 ASN cc_start: 0.8018 (p0) cc_final: 0.7346 (t0) REVERT: F 393 ASN cc_start: 0.9071 (t0) cc_final: 0.8622 (t0) REVERT: F 406 TYR cc_start: 0.7752 (m-80) cc_final: 0.6811 (m-10) REVERT: F 487 MET cc_start: 0.8369 (ttm) cc_final: 0.7997 (mtp) REVERT: F 521 TYR cc_start: 0.8764 (p90) cc_final: 0.8529 (p90) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0912 time to fit residues: 11.8992 Evaluate side-chains 82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN E 341 GLN E 344 GLN E 346 HIS E 467 ASN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN F 346 HIS F 467 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.142012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095751 restraints weight = 9694.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098686 restraints weight = 6433.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100686 restraints weight = 5057.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101558 restraints weight = 4392.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101558 restraints weight = 4084.025| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5718 Z= 0.150 Angle : 0.558 8.026 7776 Z= 0.285 Chirality : 0.039 0.133 903 Planarity : 0.004 0.039 1002 Dihedral : 8.149 45.998 966 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.18 % Allowed : 1.94 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.32), residues: 717 helix: 2.29 (0.30), residues: 285 sheet: 0.17 (0.42), residues: 147 loop : -0.18 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 315 TYR 0.011 0.001 TYR E 405 PHE 0.022 0.002 PHE F 364 HIS 0.006 0.001 HIS E 346 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5718) covalent geometry : angle 0.55787 ( 7776) hydrogen bonds : bond 0.03854 ( 272) hydrogen bonds : angle 4.34268 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 MET cc_start: 0.8726 (mmm) cc_final: 0.8295 (mmm) REVERT: D 391 ASN cc_start: 0.7970 (p0) cc_final: 0.7495 (t0) REVERT: D 397 ASN cc_start: 0.8869 (t0) cc_final: 0.8625 (t0) REVERT: D 401 LYS cc_start: 0.9384 (mmtt) cc_final: 0.9164 (mmtm) REVERT: D 444 ILE cc_start: 0.9528 (mm) cc_final: 0.9084 (tt) REVERT: D 487 MET cc_start: 0.7536 (ttm) cc_final: 0.6895 (mtp) REVERT: E 393 ASN cc_start: 0.9327 (t0) cc_final: 0.9024 (t0) REVERT: E 401 LYS cc_start: 0.9243 (mptt) cc_final: 0.9014 (mptt) REVERT: E 471 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8601 (mm-40) REVERT: E 487 MET cc_start: 0.8476 (ttp) cc_final: 0.7690 (mtp) REVERT: F 333 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8455 (tmt-80) REVERT: F 361 LYS cc_start: 0.8774 (tptt) cc_final: 0.8378 (tppt) REVERT: F 372 LEU cc_start: 0.9542 (mt) cc_final: 0.9309 (mt) REVERT: F 393 ASN cc_start: 0.9079 (t0) cc_final: 0.8648 (t0) REVERT: F 397 ASN cc_start: 0.9155 (t0) cc_final: 0.8782 (t0) REVERT: F 406 TYR cc_start: 0.7683 (m-80) cc_final: 0.7143 (m-10) REVERT: F 487 MET cc_start: 0.8363 (ttm) cc_final: 0.8120 (ttm) REVERT: F 521 TYR cc_start: 0.8775 (p90) cc_final: 0.8541 (p90) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.0946 time to fit residues: 11.9534 Evaluate side-chains 82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN D 427 HIS ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN F 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096325 restraints weight = 9681.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.099331 restraints weight = 6432.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101200 restraints weight = 5074.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102497 restraints weight = 4457.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102982 restraints weight = 4109.756| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5718 Z= 0.129 Angle : 0.543 5.826 7776 Z= 0.278 Chirality : 0.040 0.136 903 Planarity : 0.004 0.039 1002 Dihedral : 7.744 45.585 966 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.35 % Allowed : 1.06 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.32), residues: 717 helix: 2.40 (0.29), residues: 291 sheet: 0.15 (0.42), residues: 147 loop : -0.12 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 315 TYR 0.011 0.001 TYR E 405 PHE 0.014 0.001 PHE D 364 HIS 0.006 0.001 HIS F 346 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5718) covalent geometry : angle 0.54277 ( 7776) hydrogen bonds : bond 0.03721 ( 272) hydrogen bonds : angle 4.20152 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 MET cc_start: 0.8690 (mmm) cc_final: 0.8315 (mmm) REVERT: D 391 ASN cc_start: 0.7992 (p0) cc_final: 0.7494 (t0) REVERT: D 397 ASN cc_start: 0.8778 (t0) cc_final: 0.8493 (t0) REVERT: D 401 LYS cc_start: 0.9367 (mmtt) cc_final: 0.9135 (mmtm) REVERT: D 444 ILE cc_start: 0.9532 (mm) cc_final: 0.9117 (tt) REVERT: E 391 ASN cc_start: 0.7948 (p0) cc_final: 0.7725 (t0) REVERT: E 393 ASN cc_start: 0.9289 (t0) cc_final: 0.8975 (t0) REVERT: E 397 ASN cc_start: 0.9168 (t0) cc_final: 0.8773 (t0) REVERT: E 401 LYS cc_start: 0.9238 (mptt) cc_final: 0.8988 (mptt) REVERT: E 410 HIS cc_start: 0.6163 (m170) cc_final: 0.5763 (m-70) REVERT: E 471 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8565 (mm-40) REVERT: E 476 ASP cc_start: 0.8678 (t0) cc_final: 0.8465 (t0) REVERT: E 487 MET cc_start: 0.8412 (ttp) cc_final: 0.7682 (mtp) REVERT: F 372 LEU cc_start: 0.9469 (mt) cc_final: 0.9204 (mt) REVERT: F 393 ASN cc_start: 0.9050 (t0) cc_final: 0.8583 (t0) REVERT: F 397 ASN cc_start: 0.9150 (t0) cc_final: 0.8758 (t0) REVERT: F 406 TYR cc_start: 0.7671 (m-80) cc_final: 0.7076 (m-10) REVERT: F 487 MET cc_start: 0.8295 (ttm) cc_final: 0.7847 (mtp) REVERT: F 521 TYR cc_start: 0.8727 (p90) cc_final: 0.8526 (p90) outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 0.1001 time to fit residues: 13.0040 Evaluate side-chains 85 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 67 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN F 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105473 restraints weight = 9429.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104757 restraints weight = 7915.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106660 restraints weight = 6434.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106940 restraints weight = 4948.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107095 restraints weight = 4610.582| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5718 Z= 0.140 Angle : 0.562 5.413 7776 Z= 0.292 Chirality : 0.039 0.147 903 Planarity : 0.004 0.043 1002 Dihedral : 7.527 45.443 966 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.32), residues: 717 helix: 2.24 (0.29), residues: 288 sheet: 0.11 (0.42), residues: 147 loop : -0.17 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 325 TYR 0.010 0.001 TYR E 405 PHE 0.010 0.001 PHE F 534 HIS 0.005 0.001 HIS F 346 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5718) covalent geometry : angle 0.56228 ( 7776) hydrogen bonds : bond 0.03822 ( 272) hydrogen bonds : angle 4.47949 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 325 ARG cc_start: 0.7471 (mmp-170) cc_final: 0.7191 (mmp80) REVERT: D 350 MET cc_start: 0.8756 (mmm) cc_final: 0.8312 (mmm) REVERT: D 391 ASN cc_start: 0.7992 (p0) cc_final: 0.7405 (t0) REVERT: D 397 ASN cc_start: 0.8719 (t0) cc_final: 0.8475 (t0) REVERT: D 401 LYS cc_start: 0.9371 (mmtt) cc_final: 0.9137 (mmtm) REVERT: D 444 ILE cc_start: 0.9497 (mm) cc_final: 0.9073 (tt) REVERT: D 487 MET cc_start: 0.7513 (ttm) cc_final: 0.6990 (mtp) REVERT: E 391 ASN cc_start: 0.7849 (p0) cc_final: 0.7512 (t0) REVERT: E 393 ASN cc_start: 0.9159 (t0) cc_final: 0.8939 (t0) REVERT: E 397 ASN cc_start: 0.9145 (t0) cc_final: 0.8778 (t0) REVERT: E 401 LYS cc_start: 0.9209 (mptt) cc_final: 0.8971 (mptt) REVERT: F 361 LYS cc_start: 0.8802 (tptt) cc_final: 0.8321 (tppt) REVERT: F 372 LEU cc_start: 0.9505 (mt) cc_final: 0.9141 (mt) REVERT: F 393 ASN cc_start: 0.8992 (t0) cc_final: 0.8394 (t0) REVERT: F 397 ASN cc_start: 0.9128 (t0) cc_final: 0.8758 (t0) REVERT: F 406 TYR cc_start: 0.7731 (m-80) cc_final: 0.6682 (m-10) REVERT: F 487 MET cc_start: 0.8169 (ttm) cc_final: 0.7730 (mtp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0859 time to fit residues: 10.6185 Evaluate side-chains 81 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN D 427 HIS ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.145738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106014 restraints weight = 9517.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105220 restraints weight = 7619.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106965 restraints weight = 6257.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107465 restraints weight = 5106.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107938 restraints weight = 4642.029| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5718 Z= 0.130 Angle : 0.551 5.310 7776 Z= 0.287 Chirality : 0.039 0.137 903 Planarity : 0.004 0.039 1002 Dihedral : 7.260 44.872 966 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.32), residues: 717 helix: 2.23 (0.30), residues: 291 sheet: 0.14 (0.42), residues: 147 loop : -0.10 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 325 TYR 0.009 0.001 TYR D 405 PHE 0.008 0.001 PHE F 534 HIS 0.004 0.001 HIS F 346 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5718) covalent geometry : angle 0.55107 ( 7776) hydrogen bonds : bond 0.03671 ( 272) hydrogen bonds : angle 4.41822 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 MET cc_start: 0.8729 (mmm) cc_final: 0.8308 (mmm) REVERT: D 391 ASN cc_start: 0.7921 (p0) cc_final: 0.7416 (t0) REVERT: D 397 ASN cc_start: 0.8746 (t0) cc_final: 0.8488 (t0) REVERT: D 401 LYS cc_start: 0.9363 (mmtt) cc_final: 0.9131 (mmtm) REVERT: D 444 ILE cc_start: 0.9542 (mm) cc_final: 0.9098 (tt) REVERT: D 471 GLN cc_start: 0.8484 (mp-120) cc_final: 0.8133 (mp10) REVERT: D 487 MET cc_start: 0.7490 (ttm) cc_final: 0.6960 (mtp) REVERT: E 341 GLN cc_start: 0.8434 (mt0) cc_final: 0.8222 (mt0) REVERT: E 391 ASN cc_start: 0.7873 (p0) cc_final: 0.7453 (t0) REVERT: E 393 ASN cc_start: 0.9129 (t0) cc_final: 0.8863 (t0) REVERT: E 397 ASN cc_start: 0.9163 (t0) cc_final: 0.8768 (t0) REVERT: E 401 LYS cc_start: 0.9209 (mptt) cc_final: 0.8971 (mptt) REVERT: E 487 MET cc_start: 0.8382 (ttp) cc_final: 0.7762 (mtp) REVERT: F 361 LYS cc_start: 0.8850 (tptt) cc_final: 0.8331 (tppt) REVERT: F 372 LEU cc_start: 0.9496 (mt) cc_final: 0.9132 (mt) REVERT: F 393 ASN cc_start: 0.8956 (t0) cc_final: 0.8477 (t0) REVERT: F 397 ASN cc_start: 0.9148 (t0) cc_final: 0.8787 (t0) REVERT: F 406 TYR cc_start: 0.7811 (m-80) cc_final: 0.7292 (m-10) REVERT: F 487 MET cc_start: 0.8157 (ttm) cc_final: 0.7817 (mtp) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.0927 time to fit residues: 11.2450 Evaluate side-chains 83 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 GLN D 427 HIS D 452 ASN ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 GLN E 467 ASN F 313 HIS ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.139688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.092032 restraints weight = 9934.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.095057 restraints weight = 6488.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097072 restraints weight = 5057.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097844 restraints weight = 4372.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098873 restraints weight = 4086.000| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5718 Z= 0.183 Angle : 0.590 5.286 7776 Z= 0.308 Chirality : 0.040 0.150 903 Planarity : 0.004 0.041 1002 Dihedral : 7.260 44.156 966 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.18 % Allowed : 0.71 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.32), residues: 717 helix: 2.06 (0.30), residues: 291 sheet: 0.08 (0.42), residues: 147 loop : -0.17 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 325 TYR 0.012 0.001 TYR D 405 PHE 0.018 0.002 PHE D 364 HIS 0.005 0.001 HIS F 346 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 5718) covalent geometry : angle 0.58967 ( 7776) hydrogen bonds : bond 0.04141 ( 272) hydrogen bonds : angle 4.53426 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 984.83 seconds wall clock time: 17 minutes 42.93 seconds (1062.93 seconds total)