Starting phenix.real_space_refine on Wed Jun 4 22:48:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7o_61209/06_2025/9j7o_61209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7o_61209/06_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_61209/06_2025/9j7o_61209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7o_61209/06_2025/9j7o_61209.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7o_61209/06_2025/9j7o_61209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7o_61209/06_2025/9j7o_61209.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.51, per 1000 atoms: 0.81 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: 1.20 Conformation dependent library (CDL) restraints added in 509.9 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: 0.45 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: 1.10 Time building geometry restraints manager: 1.40 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: 1.320 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (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 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.028 0.001 PHE A 458 TYR 0.014 0.001 TYR A 69 ARG 0.004 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.14078 ( 252) hydrogen bonds : angle 5.34567 ( 750) SS BOND : bond 0.00229 ( 1) SS BOND : angle 1.23648 ( 2) covalent geometry : bond 0.00582 ( 4471) covalent geometry : angle 0.79285 ( 6078) *********************** 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 : 0.460 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: 0.9311 time to fit residues: 68.5420 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 : 0.626 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.0040 chunk 48 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.135156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106935 restraints weight = 4914.952| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.81 r_work: 0.3098 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1569 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= 0.121 Angle : 0.519 6.589 6080 Z= 0.270 Chirality : 0.039 0.136 666 Planarity : 0.004 0.041 729 Dihedral : 8.336 54.631 718 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (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 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.018 0.001 PHE A 79 TYR 0.019 0.001 TYR A 69 ARG 0.002 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 252) hydrogen bonds : angle 4.20802 ( 750) SS BOND : bond 0.00227 ( 1) SS BOND : angle 1.35522 ( 2) covalent geometry : bond 0.00275 ( 4471) covalent geometry : angle 0.51819 ( 6078) *********************** 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 : 0.477 Fit side-chains REVERT: A 317 LYS cc_start: 0.8063 (mttm) cc_final: 0.7678 (mtpp) REVERT: A 324 ARG cc_start: 0.7258 (ptp-110) cc_final: 0.6653 (ptp90) REVERT: A 358 ASP cc_start: 0.7700 (m-30) cc_final: 0.7488 (m-30) REVERT: A 408 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7691 (tm-30) REVERT: A 427 ARG cc_start: 0.6538 (mtp85) cc_final: 0.6184 (mtm180) REVERT: A 577 LYS cc_start: 0.6870 (ttpp) cc_final: 0.6605 (ttpt) REVERT: A 588 TRP cc_start: 0.5132 (OUTLIER) cc_final: 0.3768 (p-90) outliers start: 16 outliers final: 6 residues processed: 52 average time/residue: 1.1532 time to fit residues: 62.6751 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 : 0.486 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 0.0980 chunk 22 optimal weight: 0.0270 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.137690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109422 restraints weight = 4959.360| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.82 r_work: 0.3062 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1901 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= 0.098 Angle : 0.466 6.483 6080 Z= 0.240 Chirality : 0.038 0.122 666 Planarity : 0.004 0.039 729 Dihedral : 7.309 59.635 702 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.10 % Allowed : 18.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.38), residues: 529 helix: 1.77 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.87 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.013 0.001 PHE A 79 TYR 0.015 0.001 TYR A 69 ARG 0.002 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 252) hydrogen bonds : angle 3.99284 ( 750) SS BOND : bond 0.00187 ( 1) SS BOND : angle 1.17326 ( 2) covalent geometry : bond 0.00212 ( 4471) covalent geometry : angle 0.46577 ( 6078) *********************** 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 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.475 Fit side-chains REVERT: A 324 ARG cc_start: 0.7299 (ptp-110) cc_final: 0.6348 (ptt90) REVERT: A 408 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7728 (tm-30) REVERT: A 427 ARG cc_start: 0.6523 (mtp85) cc_final: 0.6158 (mtm180) REVERT: A 577 LYS cc_start: 0.6829 (ttpp) cc_final: 0.6504 (ttpt) REVERT: A 583 ARG cc_start: 0.6715 (mtt180) cc_final: 0.6483 (mtt180) REVERT: A 588 TRP cc_start: 0.5085 (OUTLIER) cc_final: 0.3768 (p-90) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 1.1139 time to fit residues: 65.1762 Evaluate side-chains 48 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 426 TYR 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 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.133749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105071 restraints weight = 4895.613| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.61 r_work: 0.2992 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2142 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= 0.107 Angle : 0.491 6.522 6080 Z= 0.252 Chirality : 0.038 0.128 666 Planarity : 0.004 0.039 729 Dihedral : 7.305 56.022 702 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.54 % Allowed : 18.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.38), residues: 529 helix: 1.78 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -0.87 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.014 0.001 PHE A 79 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 252) hydrogen bonds : angle 4.01299 ( 750) SS BOND : bond 0.00245 ( 1) SS BOND : angle 1.22401 ( 2) covalent geometry : bond 0.00239 ( 4471) covalent geometry : angle 0.49065 ( 6078) *********************** 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: 16 poor density : 41 time to evaluate : 0.503 Fit side-chains REVERT: A 284 ARG cc_start: 0.8102 (tpt90) cc_final: 0.7791 (tpt90) REVERT: A 324 ARG cc_start: 0.7189 (ptp-110) cc_final: 0.6280 (ptt90) REVERT: A 408 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: A 427 ARG cc_start: 0.6549 (mtp85) cc_final: 0.6161 (mtm180) REVERT: A 577 LYS cc_start: 0.6775 (ttpp) cc_final: 0.6402 (ttpt) REVERT: A 583 ARG cc_start: 0.6710 (mtt180) cc_final: 0.6412 (mtt180) REVERT: A 588 TRP cc_start: 0.5270 (OUTLIER) cc_final: 0.3792 (p-90) outliers start: 16 outliers final: 10 residues processed: 53 average time/residue: 1.1223 time to fit residues: 62.1578 Evaluate side-chains 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 192 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 289 GLN 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 45 optimal weight: 0.7980 chunk 10 optimal weight: 0.0000 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.134286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104744 restraints weight = 4928.550| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.67 r_work: 0.2963 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4472 Z= 0.109 Angle : 0.495 6.524 6080 Z= 0.254 Chirality : 0.038 0.130 666 Planarity : 0.004 0.040 729 Dihedral : 7.072 56.456 702 Min Nonbonded Distance : 2.632 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.38), residues: 529 helix: 1.84 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.86 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.014 0.001 PHE A 79 TYR 0.017 0.001 TYR A 69 ARG 0.001 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 252) hydrogen bonds : angle 4.05001 ( 750) SS BOND : bond 0.00226 ( 1) SS BOND : angle 1.32158 ( 2) covalent geometry : bond 0.00246 ( 4471) covalent geometry : angle 0.49414 ( 6078) *********************** 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: 15 poor density : 38 time to evaluate : 0.448 Fit side-chains REVERT: A 427 ARG cc_start: 0.6550 (mtp85) cc_final: 0.5993 (mtm180) REVERT: A 577 LYS cc_start: 0.6742 (ttpp) cc_final: 0.6333 (ttpt) REVERT: A 583 ARG cc_start: 0.6751 (mtt180) cc_final: 0.6449 (mtt180) REVERT: A 588 TRP cc_start: 0.5323 (OUTLIER) cc_final: 0.3914 (p-90) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 1.1624 time to fit residues: 60.6510 Evaluate side-chains 48 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 289 GLN 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 14 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 49 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.130054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099641 restraints weight = 4943.499| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.73 r_work: 0.2978 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2367 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= 0.101 Angle : 0.477 6.516 6080 Z= 0.244 Chirality : 0.038 0.128 666 Planarity : 0.004 0.038 729 Dihedral : 6.933 56.865 702 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.76 % Allowed : 17.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.38), residues: 529 helix: 1.88 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.81 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.013 0.001 PHE A 79 TYR 0.016 0.001 TYR A 69 ARG 0.001 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 252) hydrogen bonds : angle 4.00158 ( 750) SS BOND : bond 0.00196 ( 1) SS BOND : angle 1.20834 ( 2) covalent geometry : bond 0.00224 ( 4471) covalent geometry : angle 0.47614 ( 6078) *********************** 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 57 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 1.025 Fit side-chains REVERT: A 87 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8409 (tp) REVERT: A 284 ARG cc_start: 0.8132 (tpt90) cc_final: 0.7874 (tpt90) REVERT: A 427 ARG cc_start: 0.6522 (mtp85) cc_final: 0.5989 (mtm180) REVERT: A 577 LYS cc_start: 0.6726 (ttpp) cc_final: 0.6235 (ttpp) REVERT: A 583 ARG cc_start: 0.6735 (mtt180) cc_final: 0.6437 (mtt180) REVERT: A 588 TRP cc_start: 0.5306 (OUTLIER) cc_final: 0.3820 (p-90) outliers start: 17 outliers final: 11 residues processed: 53 average time/residue: 2.0151 time to fit residues: 110.7966 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 : 0.447 ------------------------------------------------------------------------------- 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 121 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 309 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.127127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.096684 restraints weight = 4957.630| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.73 r_work: 0.2827 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2388 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= 0.123 Angle : 0.516 6.485 6080 Z= 0.265 Chirality : 0.039 0.135 666 Planarity : 0.004 0.040 729 Dihedral : 7.219 57.014 702 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.38), residues: 529 helix: 1.75 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.88 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.015 0.001 PHE A 392 TYR 0.019 0.001 TYR A 69 ARG 0.001 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 252) hydrogen bonds : angle 4.08680 ( 750) SS BOND : bond 0.00250 ( 1) SS BOND : angle 1.40622 ( 2) covalent geometry : bond 0.00285 ( 4471) covalent geometry : angle 0.51583 ( 6078) *********************** 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 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.838 Fit side-chains REVERT: A 87 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 287 ASP cc_start: 0.7739 (t70) cc_final: 0.6987 (m-30) REVERT: A 427 ARG cc_start: 0.6586 (mtp85) cc_final: 0.6028 (mtm180) REVERT: A 577 LYS cc_start: 0.6825 (ttpp) cc_final: 0.6285 (ttpp) REVERT: A 583 ARG cc_start: 0.6710 (mtt180) cc_final: 0.6388 (mtt180) REVERT: A 588 TRP cc_start: 0.5250 (OUTLIER) cc_final: 0.3716 (p-90) outliers start: 16 outliers final: 10 residues processed: 51 average time/residue: 1.8926 time to fit residues: 99.9185 Evaluate side-chains 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 121 SER 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 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 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.127460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.097081 restraints weight = 4944.132| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.73 r_work: 0.2826 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2401 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= 0.121 Angle : 0.521 6.497 6080 Z= 0.266 Chirality : 0.039 0.136 666 Planarity : 0.004 0.040 729 Dihedral : 7.247 56.896 702 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.10 % Allowed : 18.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.38), residues: 529 helix: 1.75 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.88 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.015 0.001 PHE A 392 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 252) hydrogen bonds : angle 4.07205 ( 750) SS BOND : bond 0.00249 ( 1) SS BOND : angle 1.44752 ( 2) covalent geometry : bond 0.00282 ( 4471) covalent geometry : angle 0.52068 ( 6078) *********************** 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: 14 poor density : 40 time to evaluate : 0.457 Fit side-chains REVERT: A 87 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 287 ASP cc_start: 0.7763 (t70) cc_final: 0.7218 (m-30) REVERT: A 427 ARG cc_start: 0.6588 (mtp85) cc_final: 0.6031 (mtm180) REVERT: A 577 LYS cc_start: 0.6824 (ttpp) cc_final: 0.6274 (ttpp) REVERT: A 583 ARG cc_start: 0.6714 (mtt180) cc_final: 0.6499 (mtt180) REVERT: A 588 TRP cc_start: 0.5302 (OUTLIER) cc_final: 0.3745 (p-90) outliers start: 14 outliers final: 10 residues processed: 52 average time/residue: 1.0972 time to fit residues: 59.7662 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 : 0.516 ------------------------------------------------------------------------------- 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 121 SER 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 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 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.133135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.103867 restraints weight = 4879.724| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.64 r_work: 0.2956 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2434 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= 0.115 Angle : 0.513 6.633 6080 Z= 0.263 Chirality : 0.039 0.134 666 Planarity : 0.004 0.040 729 Dihedral : 7.201 57.099 702 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.32 % Allowed : 18.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.38), residues: 529 helix: 1.79 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.014 0.001 PHE A 392 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 252) hydrogen bonds : angle 4.05521 ( 750) SS BOND : bond 0.00304 ( 1) SS BOND : angle 1.31771 ( 2) covalent geometry : bond 0.00263 ( 4471) covalent geometry : angle 0.51279 ( 6078) *********************** 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: 15 poor density : 38 time to evaluate : 0.453 Fit side-chains REVERT: A 87 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 284 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7893 (tpt170) REVERT: A 287 ASP cc_start: 0.7660 (t70) cc_final: 0.7179 (m-30) REVERT: A 427 ARG cc_start: 0.6533 (mtp85) cc_final: 0.5999 (mtm180) REVERT: A 577 LYS cc_start: 0.6704 (ttpp) cc_final: 0.6154 (ttpp) REVERT: A 583 ARG cc_start: 0.6736 (mtt180) cc_final: 0.6397 (mtt180) REVERT: A 588 TRP cc_start: 0.5387 (OUTLIER) cc_final: 0.3810 (p-90) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 2.3321 time to fit residues: 120.1178 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 : 0.505 ------------------------------------------------------------------------------- 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 121 SER 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 426 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 567 GLN 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 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.125009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.094637 restraints weight = 4952.455| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.72 r_work: 0.2818 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2444 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= 0.128 Angle : 0.538 6.926 6080 Z= 0.275 Chirality : 0.040 0.138 666 Planarity : 0.004 0.040 729 Dihedral : 7.375 57.159 702 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.10 % Allowed : 18.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.38), residues: 529 helix: 1.71 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.95 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.016 0.001 PHE A 392 TYR 0.019 0.001 TYR A 69 ARG 0.001 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.05060 ( 252) hydrogen bonds : angle 4.10488 ( 750) SS BOND : bond 0.00339 ( 1) SS BOND : angle 1.31276 ( 2) covalent geometry : bond 0.00299 ( 4471) covalent geometry : angle 0.53790 ( 6078) ********************** 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: 14 poor density : 37 time to evaluate : 0.541 Fit side-chains REVERT: A 87 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 287 ASP cc_start: 0.7831 (t70) cc_final: 0.7350 (m-30) REVERT: A 427 ARG cc_start: 0.6586 (mtp85) cc_final: 0.6030 (mtm180) REVERT: A 577 LYS cc_start: 0.6823 (ttpp) cc_final: 0.6335 (ttpt) REVERT: A 583 ARG cc_start: 0.6728 (mtt180) cc_final: 0.6394 (mtt180) REVERT: A 588 TRP cc_start: 0.5335 (OUTLIER) cc_final: 0.3706 (p-90) outliers start: 14 outliers final: 11 residues processed: 47 average time/residue: 1.6280 time to fit residues: 79.7495 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 : 0.450 ------------------------------------------------------------------------------- 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 121 SER 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 442 LEU Chi-restraints excluded: chain A residue 567 GLN 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 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.133926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104821 restraints weight = 4814.018| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.63 r_work: 0.2966 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2461 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 : 0.502 6.649 6080 Z= 0.256 Chirality : 0.038 0.133 666 Planarity : 0.004 0.039 729 Dihedral : 7.172 57.644 702 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.38), residues: 529 helix: 1.83 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.95 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 PHE 0.013 0.001 PHE A 79 TYR 0.017 0.001 TYR A 69 ARG 0.001 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 252) hydrogen bonds : angle 4.03106 ( 750) SS BOND : bond 0.00288 ( 1) SS BOND : angle 1.19347 ( 2) covalent geometry : bond 0.00242 ( 4471) covalent geometry : angle 0.50144 ( 6078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3721.37 seconds wall clock time: 66 minutes 15.68 seconds (3975.68 seconds total)