Starting phenix.real_space_refine on Tue Aug 4 18:16:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrs_37788/08_2026/8wrs_37788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrs_37788/08_2026/8wrs_37788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wrs_37788/08_2026/8wrs_37788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrs_37788/08_2026/8wrs_37788.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wrs_37788/08_2026/8wrs_37788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrs_37788/08_2026/8wrs_37788.map" } resolution = 2.93 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 50 5.49 5 S 9 5.16 5 C 3596 2.51 5 N 1079 2.21 5 O 1207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5941 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4901 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 40, 'TRANS': 573} Chain breaks: 1 Chain: "B" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pyr': 5, 'rna3p_pur': 9, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 20} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 223 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 1.27, per 1000 atoms: 0.21 Number of scatterers: 5941 At special positions: 0 Unit cell: (86.46, 114.18, 89.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 50 15.00 O 1207 8.00 N 1079 7.00 C 3596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 259.7 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 52.1% alpha, 10.1% beta 10 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 23 through 36 Processing helix chain 'A' and resid 39 through 47 removed outlier: 3.789A pdb=" N VAL A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.322A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 125 through 168 removed outlier: 3.575A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.824A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.534A pdb=" N ARG A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.615A pdb=" N LYS A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 451 removed outlier: 4.115A pdb=" N ASP A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 465 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 471 through 477 Processing helix chain 'A' and resid 482 through 490 removed outlier: 3.601A pdb=" N TRP A 485 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 486 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 487 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N MET A 488 " --> pdb=" O TRP A 485 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 489 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 490 " --> pdb=" O LYS A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 490' Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 502 through 503 No H-bonds generated for 'chain 'A' and resid 502 through 503' Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 560 through 588 removed outlier: 3.744A pdb=" N ARG A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 637 through 642 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.531A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 65 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP A 308 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.051A pdb=" N THR A 365 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ILE A 647 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 594 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA A 649 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 596 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 385 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A 595 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 387 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLU A 597 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ILE A 389 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY A 417 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG A 403 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 406 through 407 Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 514 removed outlier: 3.661A pdb=" N GLU A 511 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 524 " --> pdb=" O GLU A 511 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1484 1.33 - 1.45: 1321 1.45 - 1.57: 3255 1.57 - 1.69: 97 1.69 - 1.81: 13 Bond restraints: 6170 Sorted by residual: bond pdb=" C1' DT D 1 " pdb=" N1 DT D 1 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DG C 5 " pdb=" C2' DG C 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.56e+00 bond pdb=" C3' DT C 3 " pdb=" C2' DT C 3 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.14e+00 bond pdb=" C1' DC C 7 " pdb=" N1 DC C 7 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.78e+00 ... (remaining 6165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8282 1.97 - 3.95: 250 3.95 - 5.92: 25 5.92 - 7.90: 1 7.90 - 9.87: 1 Bond angle restraints: 8559 Sorted by residual: angle pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sigma weight residual 119.70 125.17 -5.47 1.20e+00 6.94e-01 2.08e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.63e+01 ... (remaining 8554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 3538 35.50 - 71.00: 200 71.00 - 106.50: 16 106.50 - 142.00: 1 142.00 - 177.50: 2 Dihedral angle restraints: 3757 sinusoidal: 1987 harmonic: 1770 Sorted by residual: dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 71.11 160.89 1 1.70e+01 3.46e-03 6.46e+01 dihedral pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DG D -7 " ideal model delta sinusoidal sigma weight residual -140.00 37.50 -177.50 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA LEU A 109 " pdb=" C LEU A 109 " pdb=" N ASP A 110 " pdb=" CA ASP A 110 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 759 0.056 - 0.112: 155 0.112 - 0.168: 43 0.168 - 0.224: 1 0.224 - 0.280: 2 Chirality restraints: 960 Sorted by residual: chirality pdb=" CA LEU A 483 " pdb=" N LEU A 483 " pdb=" C LEU A 483 " pdb=" CB LEU A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA GLU A 582 " pdb=" N GLU A 582 " pdb=" C GLU A 582 " pdb=" CB GLU A 582 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' C B -8 " pdb=" C4' C B -8 " pdb=" O3' C B -8 " pdb=" C2' C B -8 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 957 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 226 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 227 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 118 " -0.047 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO A 119 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 273 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO A 274 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.034 5.00e-02 4.00e+02 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 816 2.75 - 3.29: 5562 3.29 - 3.83: 10224 3.83 - 4.36: 12033 4.36 - 4.90: 18953 Nonbonded interactions: 47588 Sorted by model distance: nonbonded pdb=" O2' U B -10 " pdb=" O2 U B -9 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 428 " pdb=" NH2 ARG A 431 " model vdw 2.271 3.120 nonbonded pdb=" NH2 ARG A 433 " pdb=" O ARG A 625 " model vdw 2.290 3.120 nonbonded pdb=" NH1 ARG A 260 " pdb=" O6 G B -16 " model vdw 2.297 3.120 nonbonded pdb=" NZ LYS A 273 " pdb=" N7 G B -11 " model vdw 2.299 3.200 ... (remaining 47583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.860 Find NCS groups from input model: 0.020 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.005 0.079 6170 Z= 0.321 Angle : 0.709 9.871 8559 Z= 0.475 Chirality : 0.050 0.280 960 Planarity : 0.007 0.116 922 Dihedral : 19.304 177.504 2615 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.77 % Allowed : 0.58 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.34), residues: 610 helix: 0.25 (0.32), residues: 278 sheet: -1.16 (0.57), residues: 69 loop : -0.78 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 581 TYR 0.016 0.002 TYR A 578 PHE 0.008 0.001 PHE A 401 TRP 0.010 0.001 TRP A 304 HIS 0.007 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.32 ( 6170) covalent geometry : angle 0.70887 / 0.47 ( 8559) hydrogen bonds : bond 0.18667 / 12.46 ( 255) hydrogen bonds : angle 6.84571 / 4.74 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.4593 (OUTLIER) cc_final: 0.4223 (pp) outliers start: 4 outliers final: 0 residues processed: 86 average time/residue: 0.7385 time to fit residues: 65.7101 Evaluate side-chains 68 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.0370 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.176510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139241 restraints weight = 7940.346| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.63 r_work: 0.3464 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6170 Z= 0.192 Angle : 0.675 14.188 8559 Z= 0.352 Chirality : 0.046 0.364 960 Planarity : 0.007 0.083 922 Dihedral : 22.413 178.827 1357 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.75 % Rotamer: Outliers : 2.11 % Allowed : 9.79 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.34), residues: 610 helix: 0.36 (0.31), residues: 276 sheet: -0.92 (0.56), residues: 70 loop : -0.52 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 134 TYR 0.020 0.002 TYR A 432 PHE 0.012 0.002 PHE A 16 TRP 0.011 0.001 TRP A 304 HIS 0.013 0.002 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 6170) covalent geometry : angle 0.67522 / 0.35 ( 8559) hydrogen bonds : bond 0.05193 / 3.42 ( 255) hydrogen bonds : angle 5.22410 / 3.66 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 14 LYS cc_start: 0.6690 (mmmt) cc_final: 0.6446 (mmmt) REVERT: A 273 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.5802 (tttt) REVERT: A 433 ARG cc_start: 0.7419 (ttm110) cc_final: 0.7135 (mtt-85) outliers start: 11 outliers final: 6 residues processed: 78 average time/residue: 0.7494 time to fit residues: 60.4400 Evaluate side-chains 70 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 589 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 135 HIS A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.176304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138859 restraints weight = 7901.856| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.63 r_work: 0.3461 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6170 Z= 0.188 Angle : 0.653 13.663 8559 Z= 0.337 Chirality : 0.046 0.373 960 Planarity : 0.006 0.071 922 Dihedral : 22.426 179.965 1357 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 2.11 % Allowed : 11.90 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.34), residues: 610 helix: 0.46 (0.31), residues: 276 sheet: -0.96 (0.55), residues: 70 loop : -0.53 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 134 TYR 0.018 0.002 TYR A 432 PHE 0.010 0.001 PHE A 16 TRP 0.011 0.001 TRP A 318 HIS 0.014 0.002 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 6170) covalent geometry : angle 0.65285 / 0.34 ( 8559) hydrogen bonds : bond 0.04627 / 2.99 ( 255) hydrogen bonds : angle 4.91940 / 3.45 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.199 Fit side-chains REVERT: A 12 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.5052 (pp) REVERT: A 14 LYS cc_start: 0.6763 (mmmt) cc_final: 0.6561 (mmmt) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.7199 time to fit residues: 49.3422 Evaluate side-chains 68 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.176346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140794 restraints weight = 7913.906| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.59 r_work: 0.3392 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6170 Z= 0.173 Angle : 0.633 11.395 8559 Z= 0.329 Chirality : 0.045 0.364 960 Planarity : 0.007 0.066 922 Dihedral : 22.402 179.908 1357 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 3.26 % Allowed : 13.44 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.34), residues: 610 helix: 0.55 (0.31), residues: 276 sheet: -0.89 (0.56), residues: 70 loop : -0.56 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.018 0.002 TYR A 432 PHE 0.008 0.001 PHE A 16 TRP 0.011 0.001 TRP A 318 HIS 0.008 0.002 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 6170) covalent geometry : angle 0.63292 / 0.33 ( 8559) hydrogen bonds : bond 0.04274 / 2.78 ( 255) hydrogen bonds : angle 4.82910 / 3.39 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.138 Fit side-chains REVERT: A 12 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.5083 (pp) REVERT: A 97 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6788 (tp30) REVERT: A 273 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.5950 (tttm) outliers start: 17 outliers final: 8 residues processed: 71 average time/residue: 0.6680 time to fit residues: 49.0885 Evaluate side-chains 70 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 130 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.176177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138239 restraints weight = 7944.288| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.59 r_work: 0.3420 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6170 Z= 0.151 Angle : 0.610 10.076 8559 Z= 0.317 Chirality : 0.044 0.339 960 Planarity : 0.006 0.062 922 Dihedral : 22.360 179.949 1357 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.03 % Allowed : 13.24 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.34), residues: 610 helix: 0.71 (0.32), residues: 276 sheet: -0.81 (0.57), residues: 70 loop : -0.43 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.017 0.002 TYR A 432 PHE 0.009 0.001 PHE A 16 TRP 0.011 0.001 TRP A 318 HIS 0.008 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 6170) covalent geometry : angle 0.60968 / 0.32 ( 8559) hydrogen bonds : bond 0.03816 / 2.47 ( 255) hydrogen bonds : angle 4.63210 / 3.25 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.179 Fit side-chains REVERT: A 12 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5297 (pp) REVERT: A 273 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6023 (tttm) REVERT: A 345 ARG cc_start: 0.8136 (mpt90) cc_final: 0.7773 (mpp-170) REVERT: A 539 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7491 (tp) REVERT: A 582 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7897 (mm-30) outliers start: 21 outliers final: 9 residues processed: 75 average time/residue: 0.5851 time to fit residues: 45.6911 Evaluate side-chains 76 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.176069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137933 restraints weight = 7901.736| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.63 r_work: 0.3415 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6170 Z= 0.154 Angle : 0.609 10.264 8559 Z= 0.315 Chirality : 0.043 0.348 960 Planarity : 0.006 0.062 922 Dihedral : 22.314 179.763 1357 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.61 % Allowed : 13.24 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.34), residues: 610 helix: 0.74 (0.32), residues: 278 sheet: -0.80 (0.57), residues: 70 loop : -0.45 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.017 0.002 TYR A 432 PHE 0.008 0.001 PHE A 16 TRP 0.010 0.001 TRP A 318 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6170) covalent geometry : angle 0.60916 / 0.32 ( 8559) hydrogen bonds : bond 0.03764 / 2.44 ( 255) hydrogen bonds : angle 4.50768 / 3.14 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.137 Fit side-chains REVERT: A 12 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5374 (pp) REVERT: A 97 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: A 273 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6070 (tttm) REVERT: A 421 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7704 (mp) REVERT: A 539 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7491 (tt) REVERT: A 582 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: A 642 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7142 (mtm180) outliers start: 24 outliers final: 10 residues processed: 78 average time/residue: 0.5935 time to fit residues: 48.0772 Evaluate side-chains 77 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 642 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.3980 chunk 16 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 130 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138421 restraints weight = 7906.975| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.67 r_work: 0.3422 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6170 Z= 0.145 Angle : 0.593 9.391 8559 Z= 0.308 Chirality : 0.043 0.336 960 Planarity : 0.006 0.059 922 Dihedral : 22.293 179.446 1357 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.65 % Allowed : 15.16 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.34), residues: 610 helix: 0.81 (0.32), residues: 278 sheet: -0.85 (0.56), residues: 70 loop : -0.42 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.018 0.001 TYR A 432 PHE 0.006 0.001 PHE A 22 TRP 0.011 0.001 TRP A 318 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6170) covalent geometry : angle 0.59348 / 0.31 ( 8559) hydrogen bonds : bond 0.03607 / 2.33 ( 255) hydrogen bonds : angle 4.40851 / 3.07 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.184 Fit side-chains REVERT: A 12 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5382 (pp) REVERT: A 97 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: A 273 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6067 (tttm) REVERT: A 421 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7682 (mp) REVERT: A 536 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.6152 (tpm170) REVERT: A 539 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7452 (tt) REVERT: A 582 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7828 (mm-30) outliers start: 19 outliers final: 8 residues processed: 72 average time/residue: 0.5886 time to fit residues: 44.0601 Evaluate side-chains 75 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 582 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 130 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.176231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138859 restraints weight = 7819.876| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.55 r_work: 0.3423 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6170 Z= 0.148 Angle : 0.597 11.204 8559 Z= 0.308 Chirality : 0.043 0.342 960 Planarity : 0.006 0.059 922 Dihedral : 22.270 179.064 1357 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.65 % Allowed : 15.16 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.34), residues: 610 helix: 0.83 (0.32), residues: 278 sheet: -0.87 (0.56), residues: 70 loop : -0.42 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.017 0.001 TYR A 432 PHE 0.005 0.001 PHE A 22 TRP 0.011 0.001 TRP A 318 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 6170) covalent geometry : angle 0.59717 / 0.31 ( 8559) hydrogen bonds : bond 0.03590 / 2.33 ( 255) hydrogen bonds : angle 4.38295 / 3.06 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.131 Fit side-chains REVERT: A 12 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5419 (pp) REVERT: A 97 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6890 (tp30) REVERT: A 273 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.5942 (tttp) REVERT: A 440 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6473 (tm-30) REVERT: A 536 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.6122 (tpm170) REVERT: A 539 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7313 (tt) REVERT: A 582 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7826 (mm-30) outliers start: 19 outliers final: 10 residues processed: 71 average time/residue: 0.5827 time to fit residues: 43.0047 Evaluate side-chains 76 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 130 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138910 restraints weight = 7896.453| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.64 r_work: 0.3432 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6170 Z= 0.144 Angle : 0.596 11.959 8559 Z= 0.306 Chirality : 0.042 0.338 960 Planarity : 0.005 0.058 922 Dihedral : 22.283 178.664 1357 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.84 % Allowed : 15.16 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.35), residues: 610 helix: 0.87 (0.32), residues: 278 sheet: -0.86 (0.56), residues: 69 loop : -0.35 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.018 0.001 TYR A 432 PHE 0.005 0.001 PHE A 401 TRP 0.011 0.001 TRP A 318 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6170) covalent geometry : angle 0.59553 / 0.31 ( 8559) hydrogen bonds : bond 0.03519 / 2.30 ( 255) hydrogen bonds : angle 4.32797 / 3.02 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.187 Fit side-chains REVERT: A 12 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5488 (pp) REVERT: A 97 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: A 273 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.5832 (tttt) REVERT: A 440 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6513 (tm-30) REVERT: A 536 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.6146 (tpm170) REVERT: A 539 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7313 (tt) REVERT: A 582 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7804 (mm-30) outliers start: 20 outliers final: 10 residues processed: 76 average time/residue: 0.5644 time to fit residues: 44.6728 Evaluate side-chains 79 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 595 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.0030 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 130 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139979 restraints weight = 7889.848| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.77 r_work: 0.3466 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6170 Z= 0.150 Angle : 0.607 10.932 8559 Z= 0.312 Chirality : 0.043 0.342 960 Planarity : 0.006 0.058 922 Dihedral : 22.261 178.374 1357 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.26 % Allowed : 15.93 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.35), residues: 610 helix: 0.89 (0.32), residues: 278 sheet: -0.88 (0.56), residues: 69 loop : -0.33 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 406 TYR 0.017 0.001 TYR A 432 PHE 0.005 0.001 PHE A 401 TRP 0.011 0.001 TRP A 318 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 6170) covalent geometry : angle 0.60700 / 0.31 ( 8559) hydrogen bonds : bond 0.03576 / 2.32 ( 255) hydrogen bonds : angle 4.33012 / 3.03 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.125 Fit side-chains REVERT: A 12 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5492 (pp) REVERT: A 97 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: A 273 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.5904 (tttp) REVERT: A 440 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6493 (tm-30) REVERT: A 536 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.6057 (tpm170) REVERT: A 539 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7338 (tt) REVERT: A 582 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7821 (mm-30) outliers start: 17 outliers final: 11 residues processed: 73 average time/residue: 0.5679 time to fit residues: 43.1017 Evaluate side-chains 80 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 633 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 34 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 130 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.178093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140189 restraints weight = 7839.027| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.75 r_work: 0.3471 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6170 Z= 0.143 Angle : 0.597 10.780 8559 Z= 0.308 Chirality : 0.042 0.334 960 Planarity : 0.005 0.057 922 Dihedral : 22.245 177.941 1357 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.84 % Allowed : 15.74 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.35), residues: 610 helix: 0.94 (0.32), residues: 278 sheet: -0.79 (0.57), residues: 69 loop : -0.32 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.018 0.001 TYR A 432 PHE 0.005 0.001 PHE A 401 TRP 0.011 0.001 TRP A 318 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6170) covalent geometry : angle 0.59718 / 0.31 ( 8559) hydrogen bonds : bond 0.03455 / 2.25 ( 255) hydrogen bonds : angle 4.29325 / 3.01 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.04 seconds wall clock time: 39 minutes 9.28 seconds (2349.28 seconds total)