Starting phenix.real_space_refine on Fri Dec 27 18:59:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvu_27745/12_2024/8dvu_27745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvu_27745/12_2024/8dvu_27745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvu_27745/12_2024/8dvu_27745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvu_27745/12_2024/8dvu_27745.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvu_27745/12_2024/8dvu_27745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvu_27745/12_2024/8dvu_27745.cif" } resolution = 2.9 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= -0.000 sd= 0.015 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 38 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3784 2.51 5 N 1059 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6170 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5375 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 25, 'TRANS': 643} Chain breaks: 1 Chain: "B" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 766 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 36.881 19.714 31.150 1.00 7.69 S ATOM 4596 SG CYS A 813 34.935 16.553 31.282 1.00 10.45 S ATOM 4899 SG CYS A 864 36.768 16.868 27.740 1.00 13.54 S ATOM 4938 SG CYS A 869 33.961 19.186 29.142 1.00 16.27 S Time building chain proxies: 4.87, per 1000 atoms: 0.79 Number of scatterers: 6170 At special positions: 0 Unit cell: (94.218, 94.218, 71.238, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 38 15.00 Mg 1 11.99 O 1254 8.00 N 1059 7.00 C 3784 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: 1.90 Conformation dependent library (CDL) restraints added in 866.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " Number of angles added : 6 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1274 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 49.2% alpha, 9.1% beta 18 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.673A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.629A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.792A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.705A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 558 removed outlier: 3.650A pdb=" N GLU A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 578 removed outlier: 3.632A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.929A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 746 through 769 Processing helix chain 'A' and resid 772 through 792 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.750A pdb=" N THR A 260 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP A 372 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 296 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A 322 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.381A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 6.821A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 833 removed outlier: 4.532A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 844 removed outlier: 6.277A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 2.17 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: 1358 1.33 - 1.45: 1471 1.45 - 1.57: 3416 1.57 - 1.69: 73 1.69 - 1.81: 46 Bond restraints: 6364 Sorted by residual: bond pdb=" C GLU A 716 " pdb=" O GLU A 716 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.30e-02 5.92e+03 2.59e+00 bond pdb=" C ASN A 625 " pdb=" O ASN A 625 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.26e+00 bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.69e-01 bond pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.46e-02 4.69e+03 7.81e-01 bond pdb=" CB PRO A 797 " pdb=" CG PRO A 797 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.35e-01 ... (remaining 6359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 8539 1.35 - 2.70: 176 2.70 - 4.06: 30 4.06 - 5.41: 12 5.41 - 6.76: 3 Bond angle restraints: 8760 Sorted by residual: angle pdb=" C GLY A 689 " pdb=" N ASP A 690 " pdb=" CA ASP A 690 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C GLU A 716 " pdb=" CA GLU A 716 " pdb=" CB GLU A 716 " ideal model delta sigma weight residual 111.86 108.41 3.45 1.34e+00 5.57e-01 6.62e+00 angle pdb=" N ALA A 440 " pdb=" CA ALA A 440 " pdb=" C ALA A 440 " ideal model delta sigma weight residual 110.64 114.09 -3.45 1.48e+00 4.57e-01 5.44e+00 angle pdb=" CA PRO A 797 " pdb=" C PRO A 797 " pdb=" O PRO A 797 " ideal model delta sigma weight residual 121.38 119.63 1.75 7.70e-01 1.69e+00 5.17e+00 angle pdb=" CA VAL A 332 " pdb=" CB VAL A 332 " pdb=" CG1 VAL A 332 " ideal model delta sigma weight residual 110.40 114.15 -3.75 1.70e+00 3.46e-01 4.87e+00 ... (remaining 8755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3497 16.62 - 33.23: 250 33.23 - 49.85: 99 49.85 - 66.46: 59 66.46 - 83.08: 21 Dihedral angle restraints: 3926 sinusoidal: 1964 harmonic: 1962 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 7.39 -67.39 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" CA LEU A 346 " pdb=" C LEU A 346 " pdb=" N THR A 347 " pdb=" CA THR A 347 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP A 492 " pdb=" CB ASP A 492 " pdb=" CG ASP A 492 " pdb=" OD1 ASP A 492 " ideal model delta sinusoidal sigma weight residual -30.00 -87.59 57.59 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 3923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 683 0.032 - 0.064: 227 0.064 - 0.096: 64 0.096 - 0.128: 30 0.128 - 0.160: 4 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA GLU A 716 " pdb=" N GLU A 716 " pdb=" C GLU A 716 " pdb=" CB GLU A 716 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CB ILE A 439 " pdb=" CA ILE A 439 " pdb=" CG1 ILE A 439 " pdb=" CG2 ILE A 439 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1005 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 716 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C GLU A 716 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU A 716 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 717 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.14e+00 pdb=" N PRO A 382 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 8 " -0.009 2.00e-02 2.50e+03 6.30e-03 8.92e-01 pdb=" N1 U B 8 " 0.016 2.00e-02 2.50e+03 pdb=" C2 U B 8 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U B 8 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 8 " 0.000 2.00e-02 2.50e+03 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 211 2.71 - 3.26: 5844 3.26 - 3.81: 10420 3.81 - 4.35: 13704 4.35 - 4.90: 21731 Nonbonded interactions: 51910 Sorted by model distance: nonbonded pdb="MG MG A1002 " pdb=" O2B ADP A1003 " model vdw 2.164 2.170 nonbonded pdb=" O CYS A 829 " pdb=" O2' G B 10 " model vdw 2.250 3.040 nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.301 3.120 nonbonded pdb=" NZ LYS A 814 " pdb=" OE1 GLN A 902 " model vdw 2.308 3.120 nonbonded pdb=" NZ LYS A 458 " pdb=" OE2 GLU A 751 " model vdw 2.342 3.120 ... (remaining 51905 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: 0.280 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 23.770 Find NCS groups from input model: 0.070 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:21.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.002 0.043 6364 Z= 0.146 Angle : 0.515 6.761 8760 Z= 0.290 Chirality : 0.038 0.160 1008 Planarity : 0.003 0.027 984 Dihedral : 16.456 83.078 2652 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.01 % Allowed : 10.55 % Favored : 88.44 % 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: -2.23 (0.28), residues: 665 helix: -0.12 (0.27), residues: 316 sheet: -2.08 (0.47), residues: 92 loop : -2.99 (0.27), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 908 HIS 0.002 0.000 HIS A 876 PHE 0.008 0.001 PHE A 842 TYR 0.008 0.001 TYR A 390 ARG 0.001 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.691 Fit side-chains REVERT: A 369 MET cc_start: 0.9111 (mtm) cc_final: 0.8792 (mtm) REVERT: A 385 MET cc_start: 0.8671 (mmm) cc_final: 0.8470 (mmp) REVERT: A 492 ASP cc_start: 0.7216 (t70) cc_final: 0.6800 (t0) REVERT: A 498 GLN cc_start: 0.7766 (mm110) cc_final: 0.7544 (mp10) REVERT: A 560 MET cc_start: 0.8845 (mtt) cc_final: 0.8369 (mtt) REVERT: A 761 MET cc_start: 0.8748 (ttp) cc_final: 0.8516 (ttm) REVERT: A 786 HIS cc_start: 0.8184 (t70) cc_final: 0.7883 (t70) outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 1.3667 time to fit residues: 162.6013 Evaluate side-chains 84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 800 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 393 GLN A 517 GLN A 588 GLN A 708 GLN A 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6364 Z= 0.230 Angle : 0.538 5.847 8760 Z= 0.275 Chirality : 0.041 0.164 1008 Planarity : 0.003 0.030 984 Dihedral : 15.164 77.201 1292 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.18 % Allowed : 13.74 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.30), residues: 665 helix: 0.89 (0.28), residues: 321 sheet: -1.73 (0.47), residues: 89 loop : -2.63 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 771 HIS 0.003 0.001 HIS A 623 PHE 0.009 0.001 PHE A 842 TYR 0.015 0.001 TYR A 390 ARG 0.002 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.709 Fit side-chains REVERT: A 369 MET cc_start: 0.9050 (mtm) cc_final: 0.8758 (mtm) REVERT: A 385 MET cc_start: 0.8645 (mmm) cc_final: 0.8437 (mmp) REVERT: A 425 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: A 479 MET cc_start: 0.9273 (mtp) cc_final: 0.8938 (mtp) REVERT: A 492 ASP cc_start: 0.7340 (t70) cc_final: 0.6994 (t0) REVERT: A 498 GLN cc_start: 0.7776 (mm110) cc_final: 0.7540 (mp10) REVERT: A 560 MET cc_start: 0.8908 (mtt) cc_final: 0.8397 (mtt) REVERT: A 761 MET cc_start: 0.8973 (ttp) cc_final: 0.8644 (ttm) REVERT: A 786 HIS cc_start: 0.8260 (t70) cc_final: 0.7971 (t70) REVERT: A 883 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.6522 (tm-30) REVERT: A 914 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6882 (tm-30) outliers start: 19 outliers final: 8 residues processed: 89 average time/residue: 1.4009 time to fit residues: 130.9550 Evaluate side-chains 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6364 Z= 0.173 Angle : 0.500 5.854 8760 Z= 0.254 Chirality : 0.039 0.147 1008 Planarity : 0.003 0.032 984 Dihedral : 15.091 75.194 1289 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.35 % Allowed : 14.91 % Favored : 81.74 % 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: -0.48 (0.31), residues: 665 helix: 1.45 (0.29), residues: 321 sheet: -1.36 (0.50), residues: 93 loop : -2.32 (0.31), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 771 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.012 0.001 TYR A 756 ARG 0.002 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.845 Fit side-chains REVERT: A 369 MET cc_start: 0.9044 (mtm) cc_final: 0.8753 (mtm) REVERT: A 385 MET cc_start: 0.8643 (mmm) cc_final: 0.8435 (mmp) REVERT: A 479 MET cc_start: 0.9274 (mtp) cc_final: 0.8907 (mtp) REVERT: A 492 ASP cc_start: 0.7270 (t70) cc_final: 0.6890 (t0) REVERT: A 498 GLN cc_start: 0.7779 (mm110) cc_final: 0.7507 (mp10) REVERT: A 560 MET cc_start: 0.8923 (mtt) cc_final: 0.8418 (mtt) REVERT: A 679 LYS cc_start: 0.8464 (tttt) cc_final: 0.7991 (mttp) REVERT: A 761 MET cc_start: 0.8975 (ttp) cc_final: 0.8684 (ttm) REVERT: A 786 HIS cc_start: 0.8258 (t70) cc_final: 0.7988 (t70) REVERT: A 906 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 914 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6920 (tm-30) outliers start: 20 outliers final: 7 residues processed: 95 average time/residue: 1.3771 time to fit residues: 137.0422 Evaluate side-chains 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6364 Z= 0.382 Angle : 0.632 6.390 8760 Z= 0.320 Chirality : 0.045 0.145 1008 Planarity : 0.004 0.031 984 Dihedral : 15.242 93.832 1286 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.19 % Allowed : 13.23 % Favored : 82.58 % 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: -0.64 (0.31), residues: 665 helix: 1.29 (0.29), residues: 321 sheet: -1.25 (0.50), residues: 89 loop : -2.43 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 771 HIS 0.004 0.001 HIS A 317 PHE 0.011 0.002 PHE A 842 TYR 0.019 0.002 TYR A 717 ARG 0.002 0.001 ARG A 791 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.704 Fit side-chains REVERT: A 312 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7565 (mtmm) REVERT: A 385 MET cc_start: 0.8701 (mmm) cc_final: 0.8457 (mmp) REVERT: A 447 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: A 492 ASP cc_start: 0.7396 (t70) cc_final: 0.6994 (t70) REVERT: A 498 GLN cc_start: 0.7753 (mm110) cc_final: 0.7507 (mp10) REVERT: A 560 MET cc_start: 0.8963 (mtt) cc_final: 0.8514 (mtt) REVERT: A 761 MET cc_start: 0.9070 (ttp) cc_final: 0.8703 (ttm) REVERT: A 786 HIS cc_start: 0.8263 (t70) cc_final: 0.7997 (t70) REVERT: A 883 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6649 (tm-30) REVERT: A 914 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6826 (tm-30) outliers start: 25 outliers final: 10 residues processed: 90 average time/residue: 1.2807 time to fit residues: 121.0772 Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.0070 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6364 Z= 0.204 Angle : 0.527 6.136 8760 Z= 0.268 Chirality : 0.040 0.140 1008 Planarity : 0.003 0.034 984 Dihedral : 15.184 89.299 1286 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.18 % Allowed : 15.41 % Favored : 81.41 % 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: -0.18 (0.32), residues: 665 helix: 1.72 (0.29), residues: 321 sheet: -1.07 (0.51), residues: 89 loop : -2.26 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.016 0.002 TYR A 756 ARG 0.001 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.761 Fit side-chains REVERT: A 312 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7548 (mtmm) REVERT: A 491 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6833 (mppt) REVERT: A 492 ASP cc_start: 0.7247 (t70) cc_final: 0.6854 (t70) REVERT: A 498 GLN cc_start: 0.7665 (mm110) cc_final: 0.7404 (mp10) REVERT: A 560 MET cc_start: 0.8952 (mtt) cc_final: 0.8405 (mtt) REVERT: A 679 LYS cc_start: 0.8464 (tttt) cc_final: 0.7983 (mttp) REVERT: A 761 MET cc_start: 0.9030 (ttp) cc_final: 0.8673 (ttm) REVERT: A 786 HIS cc_start: 0.8270 (t70) cc_final: 0.7968 (t70) REVERT: A 914 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6803 (tm-30) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 1.4344 time to fit residues: 132.0903 Evaluate side-chains 91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 336 GLN A 588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6364 Z= 0.221 Angle : 0.535 7.103 8760 Z= 0.271 Chirality : 0.040 0.141 1008 Planarity : 0.003 0.036 984 Dihedral : 15.198 90.711 1286 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.52 % Allowed : 15.24 % Favored : 81.24 % 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: 0.06 (0.32), residues: 665 helix: 1.84 (0.29), residues: 321 sheet: -0.75 (0.53), residues: 84 loop : -2.09 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.010 0.001 PHE A 842 TYR 0.015 0.002 TYR A 756 ARG 0.004 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.695 Fit side-chains REVERT: A 312 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7662 (mtmm) REVERT: A 479 MET cc_start: 0.9237 (mtp) cc_final: 0.8915 (mtp) REVERT: A 491 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6803 (mppt) REVERT: A 492 ASP cc_start: 0.7304 (t70) cc_final: 0.6913 (t70) REVERT: A 560 MET cc_start: 0.8969 (mtt) cc_final: 0.8414 (mtt) REVERT: A 679 LYS cc_start: 0.8465 (tttt) cc_final: 0.7979 (mttp) REVERT: A 761 MET cc_start: 0.9028 (ttp) cc_final: 0.8680 (ttm) REVERT: A 786 HIS cc_start: 0.8263 (t70) cc_final: 0.7971 (t70) REVERT: A 914 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6819 (tm-30) outliers start: 21 outliers final: 13 residues processed: 85 average time/residue: 1.3231 time to fit residues: 117.9130 Evaluate side-chains 86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6364 Z= 0.203 Angle : 0.523 7.658 8760 Z= 0.264 Chirality : 0.040 0.140 1008 Planarity : 0.003 0.036 984 Dihedral : 15.186 89.454 1286 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.69 % Allowed : 15.75 % Favored : 80.57 % 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: 0.26 (0.32), residues: 665 helix: 1.96 (0.29), residues: 321 sheet: -0.62 (0.53), residues: 96 loop : -1.98 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.018 0.002 TYR A 717 ARG 0.003 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.643 Fit side-chains REVERT: A 312 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7645 (mtmm) REVERT: A 479 MET cc_start: 0.9249 (mtp) cc_final: 0.8914 (mtp) REVERT: A 491 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6784 (mppt) REVERT: A 492 ASP cc_start: 0.7257 (t70) cc_final: 0.6663 (t0) REVERT: A 560 MET cc_start: 0.8955 (mtt) cc_final: 0.8436 (mtt) REVERT: A 679 LYS cc_start: 0.8447 (tttt) cc_final: 0.7943 (mttp) REVERT: A 761 MET cc_start: 0.9023 (ttp) cc_final: 0.8669 (ttm) REVERT: A 786 HIS cc_start: 0.8263 (t70) cc_final: 0.7962 (t70) REVERT: A 914 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6696 (tm-30) outliers start: 22 outliers final: 13 residues processed: 92 average time/residue: 1.3118 time to fit residues: 126.3907 Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.003 0.041 6364 Z= 0.189 Angle : 0.522 8.010 8760 Z= 0.264 Chirality : 0.040 0.141 1008 Planarity : 0.003 0.036 984 Dihedral : 15.169 87.342 1286 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.35 % Allowed : 16.42 % Favored : 80.23 % 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: 0.35 (0.32), residues: 665 helix: 2.02 (0.29), residues: 321 sheet: -0.56 (0.53), residues: 96 loop : -1.94 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 771 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.017 0.002 TYR A 756 ARG 0.003 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.621 Fit side-chains REVERT: A 312 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7626 (mtmm) REVERT: A 479 MET cc_start: 0.9251 (mtp) cc_final: 0.8904 (mtp) REVERT: A 491 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6742 (mppt) REVERT: A 492 ASP cc_start: 0.7237 (t70) cc_final: 0.6644 (t0) REVERT: A 546 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8531 (tpt90) REVERT: A 560 MET cc_start: 0.8958 (mtt) cc_final: 0.8462 (mtt) REVERT: A 679 LYS cc_start: 0.8444 (tttt) cc_final: 0.7944 (mttp) REVERT: A 761 MET cc_start: 0.9008 (ttp) cc_final: 0.8657 (ttm) REVERT: A 786 HIS cc_start: 0.8260 (t70) cc_final: 0.7965 (t70) REVERT: A 914 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6679 (tm-30) outliers start: 20 outliers final: 13 residues processed: 84 average time/residue: 1.3543 time to fit residues: 119.5585 Evaluate side-chains 86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6364 Z= 0.195 Angle : 0.533 8.190 8760 Z= 0.267 Chirality : 0.040 0.221 1008 Planarity : 0.003 0.036 984 Dihedral : 15.158 86.978 1285 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.52 % Allowed : 16.58 % Favored : 79.90 % 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: 0.39 (0.32), residues: 665 helix: 2.07 (0.29), residues: 321 sheet: -0.57 (0.53), residues: 96 loop : -1.93 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.017 0.002 TYR A 717 ARG 0.004 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.735 Fit side-chains REVERT: A 312 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7499 (mmtm) REVERT: A 479 MET cc_start: 0.9250 (mtp) cc_final: 0.8901 (mtp) REVERT: A 491 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6735 (mppt) REVERT: A 492 ASP cc_start: 0.7250 (t70) cc_final: 0.6659 (t0) REVERT: A 546 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8527 (tpt90) REVERT: A 560 MET cc_start: 0.8960 (mtt) cc_final: 0.8463 (mtt) REVERT: A 679 LYS cc_start: 0.8463 (tttt) cc_final: 0.7975 (mttp) REVERT: A 761 MET cc_start: 0.9014 (ttp) cc_final: 0.8660 (ttm) REVERT: A 786 HIS cc_start: 0.8262 (t70) cc_final: 0.7962 (t70) REVERT: A 914 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6715 (tt0) outliers start: 21 outliers final: 13 residues processed: 83 average time/residue: 1.4033 time to fit residues: 121.9041 Evaluate side-chains 86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6364 Z= 0.197 Angle : 0.535 8.264 8760 Z= 0.268 Chirality : 0.040 0.233 1008 Planarity : 0.003 0.036 984 Dihedral : 15.153 86.692 1285 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.85 % Allowed : 17.25 % Favored : 79.90 % 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: 0.42 (0.32), residues: 665 helix: 2.08 (0.29), residues: 321 sheet: -0.56 (0.53), residues: 96 loop : -1.90 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.019 0.002 TYR A 717 ARG 0.004 0.000 ARG A 533 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.946 Fit side-chains REVERT: A 312 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7498 (mmtm) REVERT: A 479 MET cc_start: 0.9249 (mtp) cc_final: 0.8898 (mtp) REVERT: A 491 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6734 (mppt) REVERT: A 492 ASP cc_start: 0.7247 (t70) cc_final: 0.6656 (t0) REVERT: A 546 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8528 (tpt90) REVERT: A 560 MET cc_start: 0.8963 (mtt) cc_final: 0.8467 (mtt) REVERT: A 679 LYS cc_start: 0.8470 (tttt) cc_final: 0.7994 (mttp) REVERT: A 761 MET cc_start: 0.9016 (ttp) cc_final: 0.8660 (ttm) REVERT: A 786 HIS cc_start: 0.8259 (t70) cc_final: 0.8000 (t70) REVERT: A 914 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6713 (tt0) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 1.5295 time to fit residues: 133.4975 Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.124651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.103972 restraints weight = 6370.985| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.14 r_work: 0.2918 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6364 Z= 0.249 Angle : 0.569 8.186 8760 Z= 0.286 Chirality : 0.042 0.236 1008 Planarity : 0.004 0.034 984 Dihedral : 15.205 92.889 1285 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.02 % Allowed : 17.09 % Favored : 79.90 % 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: 0.26 (0.32), residues: 665 helix: 1.95 (0.29), residues: 321 sheet: -0.62 (0.54), residues: 84 loop : -1.94 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.003 0.001 HIS A 317 PHE 0.010 0.001 PHE A 842 TYR 0.023 0.002 TYR A 717 ARG 0.004 0.000 ARG A 533 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.66 seconds wall clock time: 48 minutes 56.40 seconds (2936.40 seconds total)