Starting phenix.real_space_refine on Wed Jul 1 23:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7o_61209/07_2026/9j7o_61209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7o_61209/07_2026/9j7o_61209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7o_61209/07_2026/9j7o_61209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7o_61209/07_2026/9j7o_61209.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7o_61209/07_2026/9j7o_61209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7o_61209/07_2026/9j7o_61209.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 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 S 31 5.16 5 Cl 1 4.86 5 C 2937 2.51 5 N 647 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4344 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4241 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 102 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'CLR': 1, 'R16': 4} Classifications: {'undetermined': 5, 'water': 10} Link IDs: {None: 13} Chain breaks: 1 Time building chain proxies: 1.14, per 1000 atoms: 0.26 Number of scatterers: 4344 At special positions: 0 Unit cell: (73.1, 66.3, 95.2, 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) Cl 1 17.00 S 31 16.00 O 728 8.00 N 647 7.00 C 2937 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 113.1 milliseconds 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 970 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 75.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 4.131A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.783A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 115' Processing helix chain 'A' and resid 121 through 138 removed outlier: 4.501A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.847A pdb=" N LYS A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 232 Processing helix chain 'A' and resid 245 through 266 removed outlier: 3.523A pdb=" N THR A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.630A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.564A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.625A pdb=" N GLU A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.014A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.775A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 356 removed outlier: 3.704A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.671A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 removed outlier: 3.631A pdb=" N PHE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.076A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.643A pdb=" N VAL A 471 " --> pdb=" O CYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.503A pdb=" N ILE A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 4.054A pdb=" N LEU A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 252 hydrogen bonds defined for protein. 750 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: 0.67 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 654 1.32 - 1.44: 1317 1.44 - 1.57: 2456 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 4471 Sorted by residual: bond pdb=" N THR A 512 " pdb=" CA THR A 512 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.06e+01 bond pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta sigma weight residual 1.462 1.498 -0.036 1.18e-02 7.18e+03 9.06e+00 bond pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.18e-02 7.18e+03 8.86e+00 bond pdb=" N ILE A 521 " pdb=" CA ILE A 521 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.44e+00 bond pdb=" N VAL A 517 " pdb=" CA VAL A 517 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.44e+00 ... (remaining 4466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 5712 1.66 - 3.32: 303 3.32 - 4.98: 54 4.98 - 6.65: 8 6.65 - 8.31: 1 Bond angle restraints: 6078 Sorted by residual: angle pdb=" CA PHE A 458 " pdb=" CB PHE A 458 " pdb=" CG PHE A 458 " ideal model delta sigma weight residual 113.80 120.41 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" N LEU A 468 " pdb=" CA LEU A 468 " pdb=" C LEU A 468 " ideal model delta sigma weight residual 113.50 107.74 5.76 1.23e+00 6.61e-01 2.19e+01 angle pdb=" CA ASP A 459 " pdb=" CB ASP A 459 " pdb=" CG ASP A 459 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CA PHE A 58 " pdb=" CB PHE A 58 " pdb=" CG PHE A 58 " ideal model delta sigma weight residual 113.80 118.14 -4.34 1.00e+00 1.00e+00 1.89e+01 angle pdb=" CA GLY A 60 " pdb=" C GLY A 60 " pdb=" O GLY A 60 " ideal model delta sigma weight residual 121.60 117.86 3.74 9.70e-01 1.06e+00 1.49e+01 ... (remaining 6073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 2206 16.81 - 33.63: 279 33.63 - 50.44: 82 50.44 - 67.26: 17 67.26 - 84.07: 2 Dihedral angle restraints: 2586 sinusoidal: 1053 harmonic: 1533 Sorted by residual: dihedral pdb=" CA ASP A 486 " pdb=" CB ASP A 486 " pdb=" CG ASP A 486 " pdb=" OD1 ASP A 486 " ideal model delta sinusoidal sigma weight residual -30.00 -87.18 57.18 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB GLU A 569 " pdb=" CG GLU A 569 " pdb=" CD GLU A 569 " pdb=" OE1 GLU A 569 " ideal model delta sinusoidal sigma weight residual 0.00 84.07 -84.07 1 3.00e+01 1.11e-03 9.56e+00 dihedral pdb=" N GLN A 567 " pdb=" CA GLN A 567 " pdb=" CB GLN A 567 " pdb=" CG GLN A 567 " ideal model delta sinusoidal sigma weight residual -180.00 -120.01 -59.99 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 474 0.049 - 0.097: 138 0.097 - 0.146: 34 0.146 - 0.195: 18 0.195 - 0.243: 2 Chirality restraints: 666 Sorted by residual: chirality pdb=" CA LEU A 469 " pdb=" N LEU A 469 " pdb=" C LEU A 469 " pdb=" CB LEU A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C14 CLR A 705 " pdb=" C13 CLR A 705 " pdb=" C15 CLR A 705 " pdb=" C8 CLR A 705 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C13 CLR A 705 " pdb=" C12 CLR A 705 " pdb=" C14 CLR A 705 " pdb=" C17 CLR A 705 " both_signs ideal model delta sigma weight residual False -2.93 -2.74 -0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 663 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 577 " 0.021 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C LYS A 577 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS A 577 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR A 578 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 459 " -0.008 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C ASP A 459 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP A 459 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 460 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.70e+00 pdb=" N PRO A 208 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.023 5.00e-02 4.00e+02 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1209 2.81 - 3.34: 3916 3.34 - 3.86: 6858 3.86 - 4.38: 8070 4.38 - 4.90: 14378 Nonbonded interactions: 34431 Sorted by model distance: nonbonded pdb=" CD1 ILE A 563 " pdb=" C21 CLR A 705 " model vdw 2.292 3.880 nonbonded pdb=" N ASP A 211 " pdb=" OD1 ASP A 211 " model vdw 2.310 3.120 nonbonded pdb=" O TYR A 247 " pdb=" OG1 THR A 251 " model vdw 2.365 3.040 nonbonded pdb=" O HOH A 804 " pdb=" O HOH A 806 " model vdw 2.366 3.040 nonbonded pdb=" CG TYR A 461 " pdb=" CE1 TYR A 461 " model vdw 2.400 3.560 ... (remaining 34426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.940 Find NCS groups from input model: 0.020 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 0.036 4472 Z= 0.397 Angle : 0.793 8.308 6080 Z= 0.528 Chirality : 0.053 0.243 666 Planarity : 0.005 0.058 729 Dihedral : 16.109 84.069 1613 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.31 % Allowed : 18.36 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.38), residues: 529 helix: 1.32 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.88 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.014 0.001 TYR A 69 PHE 0.028 0.001 PHE A 458 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.40 ( 4471) covalent geometry : angle 0.79285 / 0.53 ( 6078) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 1.23648 / 0.68 ( 2) hydrogen bonds : bond 0.14078 / 7.84 ( 252) hydrogen bonds : angle 5.34567 / 3.88 ( 750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7818 (mttm) cc_final: 0.7533 (mtpp) REVERT: A 324 ARG cc_start: 0.6970 (ptp-110) cc_final: 0.6720 (ptp90) REVERT: A 408 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7396 (tt0) REVERT: A 427 ARG cc_start: 0.6575 (mtp85) cc_final: 0.6098 (mtm180) REVERT: A 537 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8259 (t) REVERT: A 577 LYS cc_start: 0.6725 (ttpp) cc_final: 0.6353 (ttpt) REVERT: A 588 TRP cc_start: 0.5017 (OUTLIER) cc_final: 0.3847 (p-90) outliers start: 24 outliers final: 13 residues processed: 70 average time/residue: 0.4409 time to fit residues: 32.3443 Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.0060 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.0470 chunk 30 optimal weight: 0.6980 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110537 restraints weight = 4961.901| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.82 r_work: 0.3137 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4472 Z= 0.105 Angle : 0.491 6.437 6080 Z= 0.254 Chirality : 0.038 0.126 666 Planarity : 0.004 0.039 729 Dihedral : 8.244 54.995 718 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.32 % Allowed : 18.81 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.38), residues: 529 helix: 1.58 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -0.92 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.016 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 4471) covalent geometry : angle 0.49026 / 0.25 ( 6078) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 1.19440 / 0.65 ( 2) hydrogen bonds : bond 0.03974 / 2.48 ( 252) hydrogen bonds : angle 4.14251 / 2.88 ( 750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.176 Fit side-chains REVERT: A 317 LYS cc_start: 0.8025 (mttm) cc_final: 0.7652 (mtpp) REVERT: A 324 ARG cc_start: 0.7273 (ptp-110) cc_final: 0.6715 (ptp90) REVERT: A 358 ASP cc_start: 0.7634 (m-30) cc_final: 0.7409 (m-30) REVERT: A 408 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7635 (tm-30) REVERT: A 427 ARG cc_start: 0.6540 (mtp85) cc_final: 0.6196 (mtm180) REVERT: A 577 LYS cc_start: 0.6848 (ttpp) cc_final: 0.6611 (ttpt) REVERT: A 588 TRP cc_start: 0.4982 (OUTLIER) cc_final: 0.3593 (p-90) outliers start: 15 outliers final: 6 residues processed: 53 average time/residue: 0.4463 time to fit residues: 24.8948 Evaluate side-chains 46 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104300 restraints weight = 4972.115| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.80 r_work: 0.2972 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4472 Z= 0.125 Angle : 0.524 6.404 6080 Z= 0.271 Chirality : 0.040 0.137 666 Planarity : 0.004 0.040 729 Dihedral : 7.723 55.597 702 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.54 % Allowed : 18.81 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.38), residues: 529 helix: 1.59 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.020 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 4471) covalent geometry : angle 0.52312 / 0.27 ( 6078) SS BOND : bond 0.00291 / 0.15 ( 1) SS BOND : angle 1.40343 / 0.76 ( 2) hydrogen bonds : bond 0.05079 / 3.19 ( 252) hydrogen bonds : angle 4.13730 / 2.89 ( 750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.162 Fit side-chains REVERT: A 324 ARG cc_start: 0.7328 (ptp-110) cc_final: 0.6387 (ptt90) REVERT: A 408 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7790 (tm-30) REVERT: A 427 ARG cc_start: 0.6575 (mtp85) cc_final: 0.6189 (mtm180) REVERT: A 577 LYS cc_start: 0.6859 (ttpp) cc_final: 0.6510 (ttpt) REVERT: A 583 ARG cc_start: 0.6709 (mtt180) cc_final: 0.6486 (mtt180) REVERT: A 588 TRP cc_start: 0.5174 (OUTLIER) cc_final: 0.3786 (p-90) outliers start: 16 outliers final: 10 residues processed: 55 average time/residue: 0.5830 time to fit residues: 33.3194 Evaluate side-chains 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101294 restraints weight = 4949.078| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.81 r_work: 0.2962 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4472 Z= 0.127 Angle : 0.530 6.497 6080 Z= 0.272 Chirality : 0.040 0.138 666 Planarity : 0.004 0.042 729 Dihedral : 7.361 57.469 700 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.32 % Allowed : 18.14 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.38), residues: 529 helix: 1.55 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.03 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.019 0.001 TYR A 69 PHE 0.016 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4471) covalent geometry : angle 0.52897 / 0.27 ( 6078) SS BOND : bond 0.00297 / 0.16 ( 1) SS BOND : angle 1.44544 / 0.78 ( 2) hydrogen bonds : bond 0.05030 / 3.18 ( 252) hydrogen bonds : angle 4.14559 / 2.88 ( 750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.182 Fit side-chains REVERT: A 87 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8456 (tp) REVERT: A 284 ARG cc_start: 0.8151 (tpt90) cc_final: 0.7842 (tpt90) REVERT: A 287 ASP cc_start: 0.7720 (t70) cc_final: 0.7109 (m-30) REVERT: A 324 ARG cc_start: 0.7257 (ptp-110) cc_final: 0.6379 (ptt90) REVERT: A 408 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: A 427 ARG cc_start: 0.6608 (mtp85) cc_final: 0.6043 (mtm180) REVERT: A 577 LYS cc_start: 0.6816 (ttpp) cc_final: 0.6416 (ttpt) REVERT: A 583 ARG cc_start: 0.6749 (mtt180) cc_final: 0.6319 (mtt180) REVERT: A 588 TRP cc_start: 0.5334 (OUTLIER) cc_final: 0.3826 (p-90) outliers start: 15 outliers final: 9 residues processed: 53 average time/residue: 0.5450 time to fit residues: 30.0799 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.099254 restraints weight = 5029.032| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.82 r_work: 0.2931 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4472 Z= 0.130 Angle : 0.537 6.498 6080 Z= 0.275 Chirality : 0.040 0.139 666 Planarity : 0.004 0.043 729 Dihedral : 7.359 57.201 700 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.10 % Allowed : 19.03 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.38), residues: 529 helix: 1.58 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.06 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.019 0.001 TYR A 69 PHE 0.016 0.002 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 4471) covalent geometry : angle 0.53611 / 0.27 ( 6078) SS BOND : bond 0.00290 / 0.15 ( 1) SS BOND : angle 1.46662 / 0.79 ( 2) hydrogen bonds : bond 0.05166 / 3.26 ( 252) hydrogen bonds : angle 4.15480 / 2.89 ( 750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.171 Fit side-chains REVERT: A 427 ARG cc_start: 0.6582 (mtp85) cc_final: 0.6029 (mtm180) REVERT: A 577 LYS cc_start: 0.6847 (ttpp) cc_final: 0.6408 (ttpt) REVERT: A 583 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6599 (mtt180) REVERT: A 588 TRP cc_start: 0.5392 (OUTLIER) cc_final: 0.3853 (p-90) outliers start: 14 outliers final: 8 residues processed: 50 average time/residue: 0.5919 time to fit residues: 30.7822 Evaluate side-chains 47 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.101633 restraints weight = 5020.629| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.82 r_work: 0.2968 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4472 Z= 0.117 Angle : 0.513 6.506 6080 Z= 0.263 Chirality : 0.039 0.136 666 Planarity : 0.004 0.042 729 Dihedral : 7.211 58.112 700 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.54 % Allowed : 18.36 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.38), residues: 529 helix: 1.65 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.04 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.018 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4471) covalent geometry : angle 0.51220 / 0.26 ( 6078) SS BOND : bond 0.00244 / 0.13 ( 1) SS BOND : angle 1.38835 / 0.75 ( 2) hydrogen bonds : bond 0.04716 / 2.97 ( 252) hydrogen bonds : angle 4.10814 / 2.85 ( 750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.150 Fit side-chains REVERT: A 87 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 284 ARG cc_start: 0.8179 (tpt90) cc_final: 0.7944 (tpt90) REVERT: A 287 ASP cc_start: 0.7728 (t70) cc_final: 0.7042 (m-30) REVERT: A 427 ARG cc_start: 0.6593 (mtp85) cc_final: 0.6041 (mtm180) REVERT: A 577 LYS cc_start: 0.6776 (ttpp) cc_final: 0.6350 (ttpt) REVERT: A 583 ARG cc_start: 0.6759 (mtt180) cc_final: 0.6456 (mtt180) REVERT: A 588 TRP cc_start: 0.5287 (OUTLIER) cc_final: 0.3823 (p-90) outliers start: 16 outliers final: 10 residues processed: 51 average time/residue: 0.5283 time to fit residues: 28.1163 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.0000 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104431 restraints weight = 4964.019| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.81 r_work: 0.2997 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4472 Z= 0.111 Angle : 0.504 6.501 6080 Z= 0.258 Chirality : 0.038 0.133 666 Planarity : 0.004 0.042 729 Dihedral : 7.133 59.061 700 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.65 % Allowed : 18.81 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.38), residues: 529 helix: 1.74 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -1.00 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 240 TYR 0.017 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 4471) covalent geometry : angle 0.50329 / 0.26 ( 6078) SS BOND : bond 0.00231 / 0.12 ( 1) SS BOND : angle 1.31928 / 0.72 ( 2) hydrogen bonds : bond 0.04498 / 2.83 ( 252) hydrogen bonds : angle 4.06834 / 2.82 ( 750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.167 Fit side-chains REVERT: A 87 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8442 (tp) REVERT: A 284 ARG cc_start: 0.8156 (tpt90) cc_final: 0.7863 (tpt90) REVERT: A 287 ASP cc_start: 0.7683 (t70) cc_final: 0.7183 (m-30) REVERT: A 427 ARG cc_start: 0.6567 (mtp85) cc_final: 0.6034 (mtm180) REVERT: A 577 LYS cc_start: 0.6797 (ttpp) cc_final: 0.6346 (ttpt) REVERT: A 583 ARG cc_start: 0.6764 (mtt180) cc_final: 0.6440 (mtt180) REVERT: A 588 TRP cc_start: 0.5253 (OUTLIER) cc_final: 0.3775 (p-90) outliers start: 12 outliers final: 8 residues processed: 49 average time/residue: 0.5256 time to fit residues: 26.8520 Evaluate side-chains 48 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.0070 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102369 restraints weight = 5004.522| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.79 r_work: 0.2995 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4472 Z= 0.113 Angle : 0.508 6.506 6080 Z= 0.260 Chirality : 0.039 0.133 666 Planarity : 0.004 0.042 729 Dihedral : 7.099 57.170 700 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.54 % Allowed : 17.92 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.38), residues: 529 helix: 1.76 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.01 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.018 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 4471) covalent geometry : angle 0.50770 / 0.26 ( 6078) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 1.25756 / 0.68 ( 2) hydrogen bonds : bond 0.04548 / 2.86 ( 252) hydrogen bonds : angle 4.06172 / 2.82 ( 750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.098 Fit side-chains REVERT: A 87 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8461 (tp) REVERT: A 287 ASP cc_start: 0.7738 (t70) cc_final: 0.7239 (m-30) REVERT: A 427 ARG cc_start: 0.6579 (mtp85) cc_final: 0.6046 (mtm180) REVERT: A 577 LYS cc_start: 0.6798 (ttpp) cc_final: 0.6341 (ttpt) REVERT: A 583 ARG cc_start: 0.6765 (mtt180) cc_final: 0.6439 (mtt180) REVERT: A 588 TRP cc_start: 0.5276 (OUTLIER) cc_final: 0.3793 (p-90) outliers start: 16 outliers final: 9 residues processed: 50 average time/residue: 0.5411 time to fit residues: 28.0999 Evaluate side-chains 49 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099710 restraints weight = 5004.703| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.80 r_work: 0.2875 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4472 Z= 0.183 Angle : 0.618 8.125 6080 Z= 0.315 Chirality : 0.043 0.164 666 Planarity : 0.005 0.046 729 Dihedral : 7.779 56.463 700 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.65 % Allowed : 18.58 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.37), residues: 529 helix: 1.42 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.22 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 263 TYR 0.022 0.002 TYR A 69 PHE 0.022 0.002 PHE A 392 TRP 0.015 0.002 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.18 ( 4471) covalent geometry : angle 0.61720 / 0.31 ( 6078) SS BOND : bond 0.00421 / 0.22 ( 1) SS BOND : angle 1.71555 / 0.92 ( 2) hydrogen bonds : bond 0.06475 / 4.11 ( 252) hydrogen bonds : angle 4.28361 / 2.99 ( 750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.163 Fit side-chains REVERT: A 87 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8462 (tp) REVERT: A 287 ASP cc_start: 0.7910 (t70) cc_final: 0.7335 (m-30) REVERT: A 324 ARG cc_start: 0.7330 (ptp-110) cc_final: 0.6475 (ptt90) REVERT: A 426 TYR cc_start: 0.4783 (OUTLIER) cc_final: 0.4065 (m-80) REVERT: A 427 ARG cc_start: 0.6595 (mtp85) cc_final: 0.5962 (mtm180) REVERT: A 577 LYS cc_start: 0.6797 (ttpp) cc_final: 0.6263 (ttpp) REVERT: A 583 ARG cc_start: 0.6798 (mtt180) cc_final: 0.6443 (mtt180) REVERT: A 588 TRP cc_start: 0.5136 (OUTLIER) cc_final: 0.3689 (p-90) outliers start: 12 outliers final: 7 residues processed: 51 average time/residue: 0.6057 time to fit residues: 32.1485 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.0000 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103954 restraints weight = 4985.332| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.81 r_work: 0.2958 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4472 Z= 0.114 Angle : 0.526 6.842 6080 Z= 0.271 Chirality : 0.039 0.131 666 Planarity : 0.004 0.043 729 Dihedral : 7.256 56.776 700 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.99 % Allowed : 19.47 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.38), residues: 529 helix: 1.63 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.07 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.017 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 4471) covalent geometry : angle 0.52580 / 0.27 ( 6078) SS BOND : bond 0.00200 / 0.11 ( 1) SS BOND : angle 1.36492 / 0.74 ( 2) hydrogen bonds : bond 0.04539 / 2.85 ( 252) hydrogen bonds : angle 4.10293 / 2.85 ( 750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.173 Fit side-chains REVERT: A 87 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 284 ARG cc_start: 0.8157 (tpt90) cc_final: 0.7930 (tpt170) REVERT: A 287 ASP cc_start: 0.7790 (t70) cc_final: 0.7302 (m-30) REVERT: A 426 TYR cc_start: 0.4854 (OUTLIER) cc_final: 0.4131 (m-80) REVERT: A 427 ARG cc_start: 0.6648 (mtp85) cc_final: 0.6064 (mtm180) REVERT: A 577 LYS cc_start: 0.6812 (ttpp) cc_final: 0.6338 (ttpt) REVERT: A 583 ARG cc_start: 0.6768 (mtt180) cc_final: 0.6425 (mtt180) REVERT: A 588 TRP cc_start: 0.5255 (OUTLIER) cc_final: 0.3746 (p-90) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.5349 time to fit residues: 26.2536 Evaluate side-chains 47 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.098494 restraints weight = 5014.325| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.84 r_work: 0.2952 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4472 Z= 0.122 Angle : 0.536 6.560 6080 Z= 0.275 Chirality : 0.039 0.128 666 Planarity : 0.004 0.042 729 Dihedral : 7.236 57.127 700 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.43 % Allowed : 18.81 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.37), residues: 529 helix: 1.64 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.08 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.019 0.001 TYR A 69 PHE 0.014 0.001 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 4471) covalent geometry : angle 0.53519 / 0.27 ( 6078) SS BOND : bond 0.00269 / 0.14 ( 1) SS BOND : angle 1.34739 / 0.73 ( 2) hydrogen bonds : bond 0.04837 / 3.05 ( 252) hydrogen bonds : angle 4.10399 / 2.85 ( 750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1531.49 seconds wall clock time: 26 minutes 53.63 seconds (1613.63 seconds total)