Starting phenix.real_space_refine on Wed Sep 17 04:42:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7o_61209/09_2025/9j7o_61209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7o_61209/09_2025/9j7o_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_61209/09_2025/9j7o_61209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7o_61209/09_2025/9j7o_61209.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7o_61209/09_2025/9j7o_61209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7o_61209/09_2025/9j7o_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-2.0-5805/lib/python3.9/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, 103 Unusual residues: {' CL': 1, 'CLR': 1, 'R16': 4} Classifications: {'undetermined': 6, 'water': 10} Link IDs: {None: 15} Time building chain proxies: 1.49, per 1000 atoms: 0.34 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: 0.42 Conformation dependent library (CDL) restraints added in 187.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.15 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: 0.71 Time building geometry restraints manager: 0.51 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.120 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:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 aren 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 covalent geometry : bond 0.00582 ( 4471) covalent geometry : angle 0.79285 ( 6078) SS BOND : bond 0.00229 ( 1) SS BOND : angle 1.23648 ( 2) hydrogen bonds : bond 0.14078 ( 252) hydrogen bonds : angle 5.34567 ( 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 : 0.174 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: 0.4669 time to fit residues: 34.2474 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 : 0.161 ------------------------------------------------------------------------------- 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: 1.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.0470 chunk 30 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106966 restraints weight = 5001.592| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.82 r_work: 0.3101 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4472 Z= 0.118 Angle : 0.518 6.418 6080 Z= 0.269 Chirality : 0.039 0.135 666 Planarity : 0.004 0.041 729 Dihedral : 8.334 54.650 718 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 aren not related in a simple way. whole: 1.19 (0.38), residues: 529 helix: 1.50 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -0.99 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.019 0.001 TYR A 69 PHE 0.018 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 covalent geometry : bond 0.00268 ( 4471) covalent geometry : angle 0.51707 ( 6078) SS BOND : bond 0.00230 ( 1) SS BOND : angle 1.34002 ( 2) hydrogen bonds : bond 0.04516 ( 252) hydrogen bonds : angle 4.19386 ( 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 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.161 Fit side-chains REVERT: A 317 LYS cc_start: 0.8064 (mttm) cc_final: 0.7680 (mtpp) REVERT: A 324 ARG cc_start: 0.7273 (ptp-110) cc_final: 0.6655 (ptp90) REVERT: A 358 ASP cc_start: 0.7694 (m-30) cc_final: 0.7480 (m-30) REVERT: A 408 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7686 (tm-30) REVERT: A 427 ARG cc_start: 0.6542 (mtp85) cc_final: 0.6184 (mtm180) REVERT: A 577 LYS cc_start: 0.6875 (ttpp) cc_final: 0.6605 (ttpt) REVERT: A 588 TRP cc_start: 0.5113 (OUTLIER) cc_final: 0.3754 (p-90) outliers start: 16 outliers final: 6 residues processed: 52 average time/residue: 0.4978 time to fit residues: 27.0283 Evaluate side-chains 44 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 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 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: 0.5980 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 0.0570 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107997 restraints weight = 4967.212| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.82 r_work: 0.3038 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4472 Z= 0.103 Angle : 0.479 6.471 6080 Z= 0.247 Chirality : 0.038 0.126 666 Planarity : 0.004 0.039 729 Dihedral : 7.396 59.350 702 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.10 % Allowed : 18.58 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.38), residues: 529 helix: 1.73 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -0.93 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.016 0.001 TYR A 69 PHE 0.013 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 covalent geometry : bond 0.00226 ( 4471) covalent geometry : angle 0.47863 ( 6078) SS BOND : bond 0.00204 ( 1) SS BOND : angle 1.24555 ( 2) hydrogen bonds : bond 0.04105 ( 252) hydrogen bonds : angle 4.02370 ( 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: 14 poor density : 44 time to evaluate : 0.166 Fit side-chains REVERT: A 324 ARG cc_start: 0.7298 (ptp-110) cc_final: 0.6359 (ptt90) REVERT: A 408 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7739 (tm-30) REVERT: A 427 ARG cc_start: 0.6539 (mtp85) cc_final: 0.6157 (mtm180) REVERT: A 577 LYS cc_start: 0.6827 (ttpp) cc_final: 0.6497 (ttpt) REVERT: A 583 ARG cc_start: 0.6721 (mtt180) cc_final: 0.6482 (mtt180) REVERT: A 588 TRP cc_start: 0.5104 (OUTLIER) cc_final: 0.3805 (p-90) outliers start: 14 outliers final: 9 residues processed: 55 average time/residue: 0.5784 time to fit residues: 32.9499 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 : 0.156 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.101828 restraints weight = 4920.320| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.61 r_work: 0.2839 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2166 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 : 0.539 6.478 6080 Z= 0.276 Chirality : 0.040 0.137 666 Planarity : 0.004 0.042 729 Dihedral : 7.635 58.930 702 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.32 % Allowed : 17.92 % 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 aren not related in a simple way. whole: 1.35 (0.38), residues: 529 helix: 1.64 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.98 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.020 0.001 TYR A 69 PHE 0.016 0.002 PHE A 392 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4471) covalent geometry : angle 0.53870 ( 6078) SS BOND : bond 0.00290 ( 1) SS BOND : angle 1.45153 ( 2) hydrogen bonds : bond 0.05158 ( 252) hydrogen bonds : angle 4.11711 ( 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 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.170 Fit side-chains REVERT: A 284 ARG cc_start: 0.8089 (tpt90) cc_final: 0.7774 (tpt90) REVERT: A 287 ASP cc_start: 0.7662 (t70) cc_final: 0.7026 (m-30) REVERT: A 324 ARG cc_start: 0.7248 (ptp-110) cc_final: 0.6311 (ptt90) REVERT: A 408 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: A 427 ARG cc_start: 0.6536 (mtp85) cc_final: 0.5960 (mtm180) REVERT: A 577 LYS cc_start: 0.6766 (ttpp) cc_final: 0.6352 (ttpt) REVERT: A 583 ARG cc_start: 0.6700 (mtt180) cc_final: 0.6268 (mtt180) REVERT: A 588 TRP cc_start: 0.5281 (OUTLIER) cc_final: 0.3783 (p-90) outliers start: 15 outliers final: 9 residues processed: 51 average time/residue: 0.5979 time to fit residues: 31.6393 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 : 0.191 ------------------------------------------------------------------------------- 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 408 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.096680 restraints weight = 5027.070| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.75 r_work: 0.2822 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2310 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= 0.126 Angle : 0.528 6.501 6080 Z= 0.271 Chirality : 0.039 0.138 666 Planarity : 0.004 0.042 729 Dihedral : 7.467 56.159 702 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.54 % Allowed : 17.70 % 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 aren not related in a simple way. whole: 1.32 (0.38), residues: 529 helix: 1.61 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.99 (0.51), 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 0.015 0.002 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4471) covalent geometry : angle 0.52777 ( 6078) SS BOND : bond 0.00250 ( 1) SS BOND : angle 1.47491 ( 2) hydrogen bonds : bond 0.05011 ( 252) hydrogen bonds : angle 4.15341 ( 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 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.114 Fit side-chains REVERT: A 87 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 427 ARG cc_start: 0.6574 (mtp85) cc_final: 0.6006 (mtm180) REVERT: A 577 LYS cc_start: 0.6832 (ttpp) cc_final: 0.6411 (ttpt) REVERT: A 583 ARG cc_start: 0.6752 (mtt180) cc_final: 0.6546 (mtt180) REVERT: A 588 TRP cc_start: 0.5356 (OUTLIER) cc_final: 0.3877 (p-90) outliers start: 16 outliers final: 9 residues processed: 51 average time/residue: 0.5619 time to fit residues: 29.8432 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 426 TYR Chi-restraints excluded: chain A residue 442 LEU 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: 1.9990 chunk 36 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.096695 restraints weight = 5042.456| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.75 r_work: 0.2822 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2394 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 : 0.521 6.650 6080 Z= 0.267 Chirality : 0.039 0.137 666 Planarity : 0.004 0.042 729 Dihedral : 7.378 57.199 702 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.32 % Allowed : 17.70 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.38), residues: 529 helix: 1.66 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.99 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 240 TYR 0.019 0.001 TYR A 69 PHE 0.015 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 covalent geometry : bond 0.00282 ( 4471) covalent geometry : angle 0.52043 ( 6078) SS BOND : bond 0.00259 ( 1) SS BOND : angle 1.41149 ( 2) hydrogen bonds : bond 0.04897 ( 252) hydrogen bonds : angle 4.10897 ( 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 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.183 Fit side-chains REVERT: A 284 ARG cc_start: 0.8232 (tpt90) cc_final: 0.7987 (tpt90) REVERT: A 287 ASP cc_start: 0.7752 (t70) cc_final: 0.7180 (m-30) REVERT: A 427 ARG cc_start: 0.6603 (mtp85) cc_final: 0.6042 (mtm180) REVERT: A 577 LYS cc_start: 0.6813 (ttpp) cc_final: 0.6399 (ttpt) REVERT: A 583 ARG cc_start: 0.6752 (mtt180) cc_final: 0.6540 (mtt180) REVERT: A 588 TRP cc_start: 0.5247 (OUTLIER) cc_final: 0.3775 (p-90) outliers start: 15 outliers final: 9 residues processed: 51 average time/residue: 0.5523 time to fit residues: 29.3756 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 : 0.172 ------------------------------------------------------------------------------- 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 121 SER 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 442 LEU 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: 0.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.094348 restraints weight = 5034.686| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.75 r_work: 0.2805 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2417 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= 0.131 Angle : 0.536 6.647 6080 Z= 0.276 Chirality : 0.040 0.138 666 Planarity : 0.004 0.043 729 Dihedral : 7.519 59.376 702 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.98 % Allowed : 17.04 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.37), residues: 529 helix: 1.62 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.01 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 423 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 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4471) covalent geometry : angle 0.53486 ( 6078) SS BOND : bond 0.00309 ( 1) SS BOND : angle 1.55813 ( 2) hydrogen bonds : bond 0.05208 ( 252) hydrogen bonds : angle 4.14242 ( 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 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.224 Fit side-chains REVERT: A 284 ARG cc_start: 0.8201 (tpt90) cc_final: 0.7887 (tpt90) REVERT: A 287 ASP cc_start: 0.7772 (t70) cc_final: 0.7183 (m-30) REVERT: A 427 ARG cc_start: 0.6613 (mtp85) cc_final: 0.6066 (mtm180) REVERT: A 577 LYS cc_start: 0.6861 (ttpp) cc_final: 0.6402 (ttpt) REVERT: A 583 ARG cc_start: 0.6757 (mtt180) cc_final: 0.6419 (mtt180) REVERT: A 588 TRP cc_start: 0.5291 (OUTLIER) cc_final: 0.3731 (p-90) outliers start: 18 outliers final: 14 residues processed: 55 average time/residue: 0.5440 time to fit residues: 31.2900 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 121 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 290 VAL 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 442 LEU Chi-restraints excluded: chain A residue 573 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: 0.3980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103073 restraints weight = 4945.164| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.62 r_work: 0.2981 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4472 Z= 0.110 Angle : 0.501 6.507 6080 Z= 0.258 Chirality : 0.039 0.134 666 Planarity : 0.004 0.042 729 Dihedral : 7.322 59.703 702 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.32 % Allowed : 17.70 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.38), residues: 529 helix: 1.75 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.96 (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 0.013 0.001 PHE A 79 TRP 0.018 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4471) covalent geometry : angle 0.50064 ( 6078) SS BOND : bond 0.00290 ( 1) SS BOND : angle 1.21375 ( 2) hydrogen bonds : bond 0.04468 ( 252) hydrogen bonds : angle 4.06988 ( 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: 15 poor density : 39 time to evaluate : 0.181 Fit side-chains REVERT: A 284 ARG cc_start: 0.8165 (tpt90) cc_final: 0.7822 (tpt90) REVERT: A 287 ASP cc_start: 0.7600 (t70) cc_final: 0.7027 (m-30) REVERT: A 427 ARG cc_start: 0.6547 (mtp85) cc_final: 0.6028 (mtm180) REVERT: A 577 LYS cc_start: 0.6748 (ttpp) cc_final: 0.6288 (ttpt) REVERT: A 583 ARG cc_start: 0.6746 (mtt180) cc_final: 0.6400 (mtt180) REVERT: A 588 TRP cc_start: 0.5317 (OUTLIER) cc_final: 0.3824 (p-90) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 0.5547 time to fit residues: 28.9088 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 : 0.194 ------------------------------------------------------------------------------- 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 289 GLN 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 442 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: 0.8980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104798 restraints weight = 4900.949| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.65 r_work: 0.2864 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4472 Z= 0.108 Angle : 0.494 6.523 6080 Z= 0.255 Chirality : 0.038 0.144 666 Planarity : 0.004 0.041 729 Dihedral : 7.223 59.047 702 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.88 % Allowed : 17.92 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.38), residues: 529 helix: 1.80 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.97 (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 0.013 0.001 PHE A 79 TRP 0.018 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4471) covalent geometry : angle 0.49405 ( 6078) SS BOND : bond 0.00244 ( 1) SS BOND : angle 1.17205 ( 2) hydrogen bonds : bond 0.04375 ( 252) hydrogen bonds : angle 4.06221 ( 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 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.158 Fit side-chains REVERT: A 284 ARG cc_start: 0.8131 (tpt90) cc_final: 0.7828 (tpt90) REVERT: A 427 ARG cc_start: 0.6485 (mtp85) cc_final: 0.5939 (mtm180) REVERT: A 577 LYS cc_start: 0.6722 (ttpp) cc_final: 0.6186 (ttpp) REVERT: A 583 ARG cc_start: 0.6696 (mtt180) cc_final: 0.6352 (mtt180) REVERT: A 588 TRP cc_start: 0.5260 (OUTLIER) cc_final: 0.3761 (p-90) outliers start: 13 outliers final: 10 residues processed: 47 average time/residue: 0.6079 time to fit residues: 29.7352 Evaluate side-chains 48 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 172 MET 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 442 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: 0.7980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.097527 restraints weight = 5028.577| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.75 r_work: 0.2838 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2487 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= 0.112 Angle : 0.508 6.622 6080 Z= 0.261 Chirality : 0.039 0.141 666 Planarity : 0.004 0.041 729 Dihedral : 7.239 58.093 702 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.88 % Allowed : 17.92 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.38), residues: 529 helix: 1.80 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.94 (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 0.013 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 covalent geometry : bond 0.00256 ( 4471) covalent geometry : angle 0.50715 ( 6078) SS BOND : bond 0.00253 ( 1) SS BOND : angle 1.24411 ( 2) hydrogen bonds : bond 0.04522 ( 252) hydrogen bonds : angle 4.06402 ( 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 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.168 Fit side-chains REVERT: A 287 ASP cc_start: 0.7752 (t70) cc_final: 0.7243 (m-30) REVERT: A 427 ARG cc_start: 0.6565 (mtp85) cc_final: 0.6021 (mtm180) REVERT: A 577 LYS cc_start: 0.6811 (ttpp) cc_final: 0.6271 (ttpp) REVERT: A 583 ARG cc_start: 0.6709 (mtt180) cc_final: 0.6371 (mtt180) REVERT: A 588 TRP cc_start: 0.5279 (OUTLIER) cc_final: 0.3775 (p-90) outliers start: 13 outliers final: 10 residues processed: 47 average time/residue: 0.6173 time to fit residues: 30.1265 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 : 0.159 ------------------------------------------------------------------------------- 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 121 SER 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 442 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: 0.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.126872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096474 restraints weight = 5013.519| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.74 r_work: 0.2929 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2497 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= 0.120 Angle : 0.522 6.811 6080 Z= 0.268 Chirality : 0.039 0.135 666 Planarity : 0.004 0.041 729 Dihedral : 7.323 57.362 702 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.65 % Allowed : 18.14 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.38), residues: 529 helix: 1.75 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.95 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 423 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 covalent geometry : bond 0.00276 ( 4471) covalent geometry : angle 0.52116 ( 6078) SS BOND : bond 0.00283 ( 1) SS BOND : angle 1.32891 ( 2) hydrogen bonds : bond 0.04805 ( 252) hydrogen bonds : angle 4.08109 ( 750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1637.82 seconds wall clock time: 28 minutes 44.78 seconds (1724.78 seconds total)