Starting phenix.real_space_refine on Sat May 10 09:53:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrs_37788/05_2025/8wrs_37788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrs_37788/05_2025/8wrs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrs_37788/05_2025/8wrs_37788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrs_37788/05_2025/8wrs_37788.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrs_37788/05_2025/8wrs_37788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrs_37788/05_2025/8wrs_37788.cif" } resolution = 2.93 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= 0.017 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.91, per 1000 atoms: 0.83 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: 1.62 Conformation dependent library (CDL) restraints added in 752.1 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: 2.03 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: 2.25 Time building geometry restraints manager: 1.88 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=" CA LEU A 483 " pdb=" C LEU A 483 " ideal model delta sigma weight residual 1.524 1.552 -0.028 1.26e-02 6.30e+03 4.99e+00 bond pdb=" C1' DT D 1 " pdb=" N1 DT D 1 " ideal model delta sigma weight residual 1.490 1.547 -0.057 3.00e-02 1.11e+03 3.64e+00 bond pdb=" CA ASP A 482 " pdb=" C ASP A 482 " ideal model delta sigma weight residual 1.523 1.537 -0.014 8.20e-03 1.49e+04 2.73e+00 bond pdb=" CA ASP A 342 " pdb=" CB ASP A 342 " ideal model delta sigma weight residual 1.526 1.550 -0.024 1.51e-02 4.39e+03 2.50e+00 bond pdb=" CG PRO A 227 " pdb=" CD PRO A 227 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.78e+00 ... (remaining 6165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8370 1.97 - 3.95: 162 3.95 - 5.92: 25 5.92 - 7.90: 1 7.90 - 9.87: 1 Bond angle restraints: 8559 Sorted by residual: angle pdb=" C LEU A 483 " pdb=" N PRO A 484 " pdb=" CA PRO A 484 " ideal model delta sigma weight residual 119.84 114.99 4.85 1.25e+00 6.40e-01 1.51e+01 angle pdb=" N GLU A 553 " pdb=" CA GLU A 553 " pdb=" CB GLU A 553 " ideal model delta sigma weight residual 110.30 115.80 -5.50 1.54e+00 4.22e-01 1.28e+01 angle pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sigma weight residual 120.20 125.17 -4.97 1.50e+00 4.44e-01 1.10e+01 angle pdb=" N LEU A 483 " pdb=" CA LEU A 483 " pdb=" C LEU A 483 " ideal model delta sigma weight residual 109.81 116.97 -7.16 2.21e+00 2.05e-01 1.05e+01 angle pdb=" C TRP A 552 " pdb=" N GLU A 553 " pdb=" CA GLU A 553 " ideal model delta sigma weight residual 120.68 115.19 5.49 1.70e+00 3.46e-01 1.04e+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: 806 0.056 - 0.112: 133 0.112 - 0.168: 18 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: 4.460 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 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 : 0.004 0.057 6170 Z= 0.192 Angle : 0.646 9.871 8559 Z= 0.345 Chirality : 0.043 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 (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: -0.62 (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 TRP 0.010 0.001 TRP A 304 HIS 0.007 0.001 HIS A 498 PHE 0.008 0.001 PHE A 401 TYR 0.016 0.002 TYR A 578 ARG 0.006 0.001 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.18667 ( 255) hydrogen bonds : angle 6.84571 ( 681) covalent geometry : bond 0.00430 ( 6170) covalent geometry : angle 0.64574 ( 8559) *********************** 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 : 0.567 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: 1.6621 time to fit residues: 147.9481 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 : 0.588 ------------------------------------------------------------------------------- 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 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4152 r_free = 0.4152 target = 0.177417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140299 restraints weight = 7843.987| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.64 r_work: 0.3480 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1086 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= 0.161 Angle : 0.629 12.160 8559 Z= 0.322 Chirality : 0.041 0.173 960 Planarity : 0.006 0.080 922 Dihedral : 22.391 178.026 1357 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.50 % Allowed : 9.40 % 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 (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: -0.16 (0.34), residues: 610 helix: 0.54 (0.32), residues: 276 sheet: -0.82 (0.56), residues: 70 loop : -0.45 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 304 HIS 0.017 0.002 HIS A 498 PHE 0.013 0.001 PHE A 16 TYR 0.020 0.002 TYR A 432 ARG 0.007 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 255) hydrogen bonds : angle 4.95281 ( 681) covalent geometry : bond 0.00363 ( 6170) covalent geometry : angle 0.62852 ( 8559) *********************** 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 85 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.5807 (tttt) REVERT: A 440 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6307 (tm-30) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 1.6320 time to fit residues: 131.9963 Evaluate side-chains 68 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4142 r_free = 0.4142 target = 0.176583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131924 restraints weight = 7849.548| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.75 r_work: 0.3434 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1400 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= 0.163 Angle : 0.601 10.718 8559 Z= 0.306 Chirality : 0.041 0.195 960 Planarity : 0.006 0.068 922 Dihedral : 22.303 178.637 1357 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.11 % Allowed : 13.44 % Favored : 84.45 % 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: -0.03 (0.34), residues: 610 helix: 0.70 (0.32), residues: 276 sheet: -0.78 (0.56), residues: 70 loop : -0.46 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.013 0.002 HIS A 498 PHE 0.009 0.001 PHE A 16 TYR 0.018 0.002 TYR A 432 ARG 0.004 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 255) hydrogen bonds : angle 4.60747 ( 681) covalent geometry : bond 0.00372 ( 6170) covalent geometry : angle 0.60118 ( 8559) *********************** 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 77 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.5385 (pp) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 1.4895 time to fit residues: 110.1393 Evaluate side-chains 70 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 400 GLU 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 32 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4133 r_free = 0.4133 target = 0.175834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130851 restraints weight = 7925.066| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.77 r_work: 0.3424 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1593 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= 0.190 Angle : 0.616 10.238 8559 Z= 0.313 Chirality : 0.043 0.199 960 Planarity : 0.006 0.065 922 Dihedral : 22.292 178.071 1357 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.75 % Rotamer: Outliers : 2.88 % Allowed : 14.40 % 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 (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: -0.02 (0.34), residues: 610 helix: 0.70 (0.32), residues: 278 sheet: -0.79 (0.57), residues: 69 loop : -0.44 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.008 0.002 HIS A 498 PHE 0.009 0.001 PHE A 16 TYR 0.019 0.002 TYR A 432 ARG 0.005 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 255) hydrogen bonds : angle 4.52928 ( 681) covalent geometry : bond 0.00437 ( 6170) covalent geometry : angle 0.61582 ( 8559) *********************** 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 74 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5544 (pp) REVERT: A 273 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6096 (tttm) REVERT: A 440 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6352 (tm-30) REVERT: A 539 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7461 (tt) outliers start: 15 outliers final: 8 residues processed: 68 average time/residue: 1.5787 time to fit residues: 111.5804 Evaluate side-chains 69 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 387 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 539 LEU 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 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 0.0070 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 130 ASN A 269 ASN A 472 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138852 restraints weight = 7869.160| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.55 r_work: 0.3451 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6170 Z= 0.152 Angle : 0.575 9.675 8559 Z= 0.292 Chirality : 0.041 0.198 960 Planarity : 0.005 0.060 922 Dihedral : 22.262 178.546 1357 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.22 % Allowed : 13.44 % Favored : 82.34 % 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: 0.12 (0.34), residues: 610 helix: 0.85 (0.32), residues: 278 sheet: -0.66 (0.56), residues: 70 loop : -0.42 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.004 0.001 HIS A 498 PHE 0.006 0.001 PHE A 16 TYR 0.018 0.001 TYR A 432 ARG 0.008 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 255) hydrogen bonds : angle 4.33128 ( 681) covalent geometry : bond 0.00349 ( 6170) covalent geometry : angle 0.57462 ( 8559) *********************** 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 80 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5559 (pp) REVERT: A 273 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.5811 (tttt) REVERT: A 345 ARG cc_start: 0.7938 (mpt90) cc_final: 0.7494 (mpt90) REVERT: A 421 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7676 (mp) REVERT: A 539 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7354 (tt) outliers start: 22 outliers final: 10 residues processed: 73 average time/residue: 1.4871 time to fit residues: 113.0978 Evaluate side-chains 74 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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 421 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 633 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.176333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131794 restraints weight = 7816.964| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.73 r_work: 0.3443 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1861 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= 0.169 Angle : 0.583 9.711 8559 Z= 0.296 Chirality : 0.041 0.186 960 Planarity : 0.005 0.059 922 Dihedral : 22.220 178.943 1357 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.75 % Rotamer: Outliers : 3.84 % Allowed : 13.63 % Favored : 82.53 % 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: 0.16 (0.35), residues: 610 helix: 0.85 (0.32), residues: 278 sheet: -0.71 (0.57), residues: 69 loop : -0.35 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 318 HIS 0.005 0.001 HIS A 498 PHE 0.007 0.001 PHE A 401 TYR 0.018 0.002 TYR A 432 ARG 0.004 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 255) hydrogen bonds : angle 4.30092 ( 681) covalent geometry : bond 0.00389 ( 6170) covalent geometry : angle 0.58338 ( 8559) *********************** 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 83 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5644 (pp) REVERT: A 273 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.5787 (tttt) REVERT: A 345 ARG cc_start: 0.7959 (mpt90) cc_final: 0.7508 (mpt90) REVERT: A 421 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7676 (mp) REVERT: A 539 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7349 (tt) outliers start: 20 outliers final: 11 residues processed: 74 average time/residue: 1.5045 time to fit residues: 115.8094 Evaluate side-chains 76 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 366 ARG Chi-restraints excluded: chain A residue 370 SER 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 589 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4130 r_free = 0.4130 target = 0.175608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130983 restraints weight = 7819.587| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.73 r_work: 0.3428 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6170 Z= 0.198 Angle : 0.613 9.889 8559 Z= 0.311 Chirality : 0.043 0.214 960 Planarity : 0.006 0.058 922 Dihedral : 22.226 179.235 1357 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.43 % Favored : 95.41 % Rotamer: Outliers : 3.84 % Allowed : 14.59 % Favored : 81.57 % 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: 0.10 (0.35), residues: 610 helix: 0.82 (0.32), residues: 278 sheet: -0.91 (0.56), residues: 69 loop : -0.34 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 249 HIS 0.005 0.001 HIS A 360 PHE 0.008 0.001 PHE A 635 TYR 0.018 0.002 TYR A 432 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 255) hydrogen bonds : angle 4.35435 ( 681) covalent geometry : bond 0.00458 ( 6170) covalent geometry : angle 0.61349 ( 8559) *********************** 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 80 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5670 (pp) REVERT: A 273 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.5881 (tttt) REVERT: A 345 ARG cc_start: 0.7984 (mpt90) cc_final: 0.7511 (mpt90) REVERT: A 421 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 539 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7369 (tt) outliers start: 20 outliers final: 10 residues processed: 72 average time/residue: 1.4538 time to fit residues: 108.9541 Evaluate side-chains 72 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 366 ARG Chi-restraints excluded: chain A residue 370 SER 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 421 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.0020 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 130 ASN A 135 HIS A 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137534 restraints weight = 7788.588| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.78 r_work: 0.3415 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.004 0.034 6170 Z= 0.168 Angle : 0.588 9.523 8559 Z= 0.299 Chirality : 0.041 0.193 960 Planarity : 0.005 0.057 922 Dihedral : 22.226 179.564 1357 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 3.65 % Allowed : 14.59 % Favored : 81.77 % 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: 0.12 (0.35), residues: 610 helix: 0.87 (0.32), residues: 279 sheet: -0.93 (0.57), residues: 69 loop : -0.37 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 249 HIS 0.004 0.001 HIS A 360 PHE 0.006 0.001 PHE A 635 TYR 0.018 0.002 TYR A 432 ARG 0.005 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 255) hydrogen bonds : angle 4.24961 ( 681) covalent geometry : bond 0.00386 ( 6170) covalent geometry : angle 0.58846 ( 8559) *********************** 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 79 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5591 (pp) REVERT: A 273 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6042 (tttm) REVERT: A 345 ARG cc_start: 0.7984 (mpt90) cc_final: 0.7529 (mtt90) REVERT: A 421 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 440 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6555 (tm-30) REVERT: A 539 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7388 (tt) outliers start: 19 outliers final: 11 residues processed: 71 average time/residue: 1.4054 time to fit residues: 104.0017 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 : 0.593 ------------------------------------------------------------------------------- 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 366 ARG Chi-restraints excluded: chain A residue 370 SER 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 589 CYS Chi-restraints excluded: chain A residue 595 VAL 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 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4122 r_free = 0.4122 target = 0.174926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130217 restraints weight = 7876.635| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.74 r_work: 0.3419 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6170 Z= 0.211 Angle : 0.623 10.037 8559 Z= 0.315 Chirality : 0.043 0.213 960 Planarity : 0.006 0.058 922 Dihedral : 22.222 179.818 1357 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.59 % Favored : 95.25 % Rotamer: Outliers : 3.84 % Allowed : 14.59 % Favored : 81.57 % 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: -0.03 (0.34), residues: 610 helix: 0.74 (0.32), residues: 279 sheet: -1.15 (0.56), residues: 69 loop : -0.40 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 249 HIS 0.005 0.001 HIS A 383 PHE 0.008 0.001 PHE A 635 TYR 0.018 0.002 TYR A 432 ARG 0.004 0.000 ARG A 567 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 255) hydrogen bonds : angle 4.34961 ( 681) covalent geometry : bond 0.00488 ( 6170) covalent geometry : angle 0.62285 ( 8559) *********************** 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 82 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5717 (pp) REVERT: A 273 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6072 (tttm) REVERT: A 345 ARG cc_start: 0.8006 (mpt90) cc_final: 0.7520 (mtt90) REVERT: A 421 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7671 (mp) REVERT: A 539 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7429 (tt) outliers start: 20 outliers final: 11 residues processed: 74 average time/residue: 1.4890 time to fit residues: 114.8134 Evaluate side-chains 76 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 366 ARG Chi-restraints excluded: chain A residue 370 SER 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 589 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 8 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 58 optimal weight: 0.0470 chunk 25 optimal weight: 0.0070 chunk 20 optimal weight: 0.5980 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4185 r_free = 0.4185 target = 0.180755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143665 restraints weight = 7854.672| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.73 r_work: 0.3497 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6170 Z= 0.108 Angle : 0.535 8.370 8559 Z= 0.274 Chirality : 0.038 0.178 960 Planarity : 0.005 0.056 922 Dihedral : 22.196 178.764 1357 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.11 % Allowed : 16.31 % Favored : 81.57 % 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: 0.41 (0.35), residues: 610 helix: 1.11 (0.32), residues: 281 sheet: -0.72 (0.58), residues: 70 loop : -0.26 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 249 HIS 0.005 0.001 HIS A 632 PHE 0.005 0.001 PHE A 350 TYR 0.017 0.001 TYR A 432 ARG 0.005 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.02780 ( 255) hydrogen bonds : angle 3.91159 ( 681) covalent geometry : bond 0.00243 ( 6170) covalent geometry : angle 0.53532 ( 8559) ********************** 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 79 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5522 (pp) REVERT: A 66 LEU cc_start: 0.8332 (mt) cc_final: 0.8109 (mp) REVERT: A 273 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.5310 (tttt) REVERT: A 344 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7404 (ttpt) REVERT: A 345 ARG cc_start: 0.7845 (mpt90) cc_final: 0.7560 (mtt90) outliers start: 11 outliers final: 3 residues processed: 74 average time/residue: 1.4971 time to fit residues: 115.3204 Evaluate side-chains 74 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 366 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 589 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 51 optimal weight: 0.0000 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4145 r_free = 0.4145 target = 0.176916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132261 restraints weight = 7903.342| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.74 r_work: 0.3447 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2246 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 : 0.598 9.152 8559 Z= 0.300 Chirality : 0.041 0.182 960 Planarity : 0.005 0.057 922 Dihedral : 22.102 178.797 1357 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.43 % Favored : 95.41 % Rotamer: Outliers : 2.30 % Allowed : 16.70 % 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 (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: 0.31 (0.35), residues: 610 helix: 1.03 (0.32), residues: 281 sheet: -0.78 (0.57), residues: 70 loop : -0.30 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 249 HIS 0.004 0.001 HIS A 383 PHE 0.007 0.001 PHE A 401 TYR 0.018 0.002 TYR A 432 ARG 0.003 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 255) hydrogen bonds : angle 4.08019 ( 681) covalent geometry : bond 0.00400 ( 6170) covalent geometry : angle 0.59790 ( 8559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5582.74 seconds wall clock time: 96 minutes 28.67 seconds (5788.67 seconds total)