Starting phenix.real_space_refine on Fri Dec 27 21:41:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zox_14849/12_2024/7zox_14849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zox_14849/12_2024/7zox_14849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zox_14849/12_2024/7zox_14849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zox_14849/12_2024/7zox_14849.map" model { file = "/net/cci-nas-00/data/ceres_data/7zox_14849/12_2024/7zox_14849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zox_14849/12_2024/7zox_14849.cif" } resolution = 4.4 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= 0.002 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4277 2.51 5 N 1179 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6772 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4923 Classifications: {'peptide': 607} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 5 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 884 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Time building chain proxies: 4.25, per 1000 atoms: 0.63 Number of scatterers: 6772 At special positions: 0 Unit cell: (115.926, 115.092, 125.934, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1275 8.00 N 1179 7.00 C 4277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 96 " distance=2.04 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: 1.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 53.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.631A pdb=" N LEU A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.962A pdb=" N ASP A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 248 through 275 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.725A pdb=" N ARG A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 331 through 342 removed outlier: 3.964A pdb=" N ALA A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.891A pdb=" N ASN A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 380 Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.600A pdb=" N ARG A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 420 Processing helix chain 'A' and resid 437 through 449 Processing helix chain 'A' and resid 452 through 457 removed outlier: 4.306A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 457 " --> pdb=" O HIS A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 457' Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.581A pdb=" N THR A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.754A pdb=" N PHE A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 528 through 538 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.840A pdb=" N ALA A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 565 through 578 removed outlier: 4.349A pdb=" N GLU A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.913A pdb=" N PHE A 602 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'A' and resid 622 through 633 Processing helix chain 'A' and resid 635 through 648 removed outlier: 3.700A pdb=" N LYS A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 653 removed outlier: 4.217A pdb=" N SER A 652 " --> pdb=" O PRO A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 678 Processing helix chain 'A' and resid 683 through 706 removed outlier: 4.051A pdb=" N THR A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 717 removed outlier: 3.502A pdb=" N SER A 711 " --> pdb=" O HIS A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 735 removed outlier: 3.841A pdb=" N PHE A 735 " --> pdb=" O ARG A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 764 removed outlier: 3.572A pdb=" N ASN A 745 " --> pdb=" O GLU A 741 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 747 " --> pdb=" O ARG A 743 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU A 748 " --> pdb=" O HIS A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 798 Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.527A pdb=" N ASN A 809 " --> pdb=" O SER A 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.510A pdb=" N THR B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.520A pdb=" N ASP B 113 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 101 through 107 removed outlier: 3.968A pdb=" N ALA C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 15 removed outlier: 5.729A pdb=" N ARG B 40 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 8 removed outlier: 3.546A pdb=" N SER C 26 " --> pdb=" O GLN C 4 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 6 " --> pdb=" O VAL C 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.759A pdb=" N THR C 120 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG C 39 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2252 1.34 - 1.46: 1333 1.46 - 1.58: 3240 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 6893 Sorted by residual: bond pdb=" CA HIS A 744 " pdb=" C HIS A 744 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.72e-02 3.38e+03 3.04e+00 bond pdb=" C VAL A 650 " pdb=" O VAL A 650 " ideal model delta sigma weight residual 1.241 1.223 0.018 1.19e-02 7.06e+03 2.29e+00 bond pdb=" CA ARG A 246 " pdb=" C ARG A 246 " ideal model delta sigma weight residual 1.522 1.498 0.023 1.72e-02 3.38e+03 1.82e+00 bond pdb=" C LEU A 364 " pdb=" N SER A 365 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.47e-02 4.63e+03 1.56e+00 bond pdb=" CA ASP A 399 " pdb=" C ASP A 399 " ideal model delta sigma weight residual 1.532 1.522 0.011 9.60e-03 1.09e+04 1.29e+00 ... (remaining 6888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 8680 1.33 - 2.66: 528 2.66 - 3.98: 72 3.98 - 5.31: 16 5.31 - 6.64: 6 Bond angle restraints: 9302 Sorted by residual: angle pdb=" N SER C 31 " pdb=" CA SER C 31 " pdb=" C SER C 31 " ideal model delta sigma weight residual 114.75 109.42 5.33 1.26e+00 6.30e-01 1.79e+01 angle pdb=" N ASP B 32 " pdb=" CA ASP B 32 " pdb=" C ASP B 32 " ideal model delta sigma weight residual 114.56 109.41 5.15 1.27e+00 6.20e-01 1.64e+01 angle pdb=" N ASN A 737 " pdb=" CA ASN A 737 " pdb=" C ASN A 737 " ideal model delta sigma weight residual 114.09 107.96 6.13 1.55e+00 4.16e-01 1.56e+01 angle pdb=" C ASN A 528 " pdb=" N PHE A 529 " pdb=" CA PHE A 529 " ideal model delta sigma weight residual 120.82 125.40 -4.58 1.50e+00 4.44e-01 9.34e+00 angle pdb=" C GLY A 450 " pdb=" N GLU A 451 " pdb=" CA GLU A 451 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.10e+00 ... (remaining 9297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 3683 17.28 - 34.57: 386 34.57 - 51.85: 68 51.85 - 69.13: 22 69.13 - 86.41: 16 Dihedral angle restraints: 4175 sinusoidal: 1696 harmonic: 2479 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 21.47 71.53 1 1.00e+01 1.00e-02 6.56e+01 dihedral pdb=" CA GLU A 451 " pdb=" C GLU A 451 " pdb=" N SER A 452 " pdb=" CA SER A 452 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PHE A 735 " pdb=" C PHE A 735 " pdb=" N ARG A 736 " pdb=" CA ARG A 736 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 547 0.026 - 0.051: 285 0.051 - 0.077: 127 0.077 - 0.102: 53 0.102 - 0.128: 17 Chirality restraints: 1029 Sorted by residual: chirality pdb=" CA VAL C 38 " pdb=" N VAL C 38 " pdb=" C VAL C 38 " pdb=" CB VAL C 38 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA HIS A 492 " pdb=" N HIS A 492 " pdb=" C HIS A 492 " pdb=" CB HIS A 492 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 314 " pdb=" N ILE A 314 " pdb=" C ILE A 314 " pdb=" CB ILE A 314 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1026 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 656 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A 657 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 657 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 657 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 42 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO B 43 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 721 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 722 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 722 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 722 " -0.022 5.00e-02 4.00e+02 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1119 2.75 - 3.29: 7223 3.29 - 3.83: 11255 3.83 - 4.36: 13389 4.36 - 4.90: 22056 Nonbonded interactions: 55042 Sorted by model distance: nonbonded pdb=" NH2 ARG A 482 " pdb=" OD2 ASP B 101 " model vdw 2.219 3.120 nonbonded pdb=" O GLN A 653 " pdb=" NH1 ARG A 661 " model vdw 2.221 3.120 nonbonded pdb=" O ASP A 781 " pdb=" OG SER A 784 " model vdw 2.236 3.040 nonbonded pdb=" OG SER A 724 " pdb=" OD1 ASP A 726 " model vdw 2.238 3.040 nonbonded pdb=" O ASN C 53 " pdb=" NH1 ARG C 72 " model vdw 2.240 3.120 ... (remaining 55037 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.890 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6893 Z= 0.305 Angle : 0.722 6.641 9302 Z= 0.450 Chirality : 0.040 0.128 1029 Planarity : 0.005 0.069 1206 Dihedral : 15.618 86.413 2574 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % 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: -4.40 (0.22), residues: 836 helix: -2.76 (0.19), residues: 402 sheet: -2.88 (0.48), residues: 91 loop : -2.94 (0.27), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 416 HIS 0.007 0.001 HIS A 492 PHE 0.023 0.002 PHE A 552 TYR 0.018 0.002 TYR A 192 ARG 0.003 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8106 (mtm) cc_final: 0.7871 (mtm) REVERT: A 293 LEU cc_start: 0.9347 (tp) cc_final: 0.8919 (mt) REVERT: A 320 TRP cc_start: 0.8141 (m100) cc_final: 0.7277 (m100) REVERT: A 344 HIS cc_start: 0.8570 (p-80) cc_final: 0.8367 (p-80) REVERT: A 349 PHE cc_start: 0.8816 (t80) cc_final: 0.8503 (t80) REVERT: A 504 LEU cc_start: 0.8302 (mt) cc_final: 0.8038 (mt) REVERT: A 602 PHE cc_start: 0.8199 (p90) cc_final: 0.7702 (p90) REVERT: A 641 GLU cc_start: 0.8709 (pt0) cc_final: 0.8196 (pt0) REVERT: A 667 MET cc_start: 0.8558 (tpt) cc_final: 0.8259 (tpp) REVERT: A 697 ILE cc_start: 0.8972 (mt) cc_final: 0.8745 (mt) REVERT: A 702 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8518 (tp30) REVERT: A 703 TYR cc_start: 0.8899 (t80) cc_final: 0.8051 (t80) REVERT: A 707 HIS cc_start: 0.7666 (m90) cc_final: 0.5965 (m-70) REVERT: A 716 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8584 (mm-30) REVERT: A 754 MET cc_start: 0.8998 (tpt) cc_final: 0.8721 (tpt) REVERT: A 803 ARG cc_start: 0.8778 (mmt180) cc_final: 0.7858 (tpt170) REVERT: B 32 ASP cc_start: 0.7800 (p0) cc_final: 0.7589 (p0) REVERT: B 38 TRP cc_start: 0.7008 (m100) cc_final: 0.6805 (m100) REVERT: B 55 LYS cc_start: 0.8107 (ptmm) cc_final: 0.7701 (ttpp) REVERT: B 85 MET cc_start: 0.8464 (mtm) cc_final: 0.8091 (mtm) REVERT: C 82 GLN cc_start: 0.7548 (tp40) cc_final: 0.6900 (tp40) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2468 time to fit residues: 60.8609 Evaluate side-chains 143 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 292 ASN A 337 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS A 457 ASN A 745 ASN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 79 ASN C 77 ASN C 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6893 Z= 0.180 Angle : 0.573 5.903 9302 Z= 0.308 Chirality : 0.040 0.142 1029 Planarity : 0.004 0.050 1206 Dihedral : 4.996 22.919 938 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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: -2.29 (0.27), residues: 836 helix: -0.61 (0.24), residues: 416 sheet: -2.53 (0.49), residues: 96 loop : -2.30 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 37 HIS 0.003 0.001 HIS A 492 PHE 0.019 0.001 PHE A 796 TYR 0.028 0.002 TYR A 262 ARG 0.007 0.001 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9311 (tp) cc_final: 0.8873 (mt) REVERT: A 320 TRP cc_start: 0.8335 (m100) cc_final: 0.7066 (m100) REVERT: A 344 HIS cc_start: 0.8475 (p-80) cc_final: 0.8226 (p-80) REVERT: A 349 PHE cc_start: 0.8714 (t80) cc_final: 0.8470 (t80) REVERT: A 392 TYR cc_start: 0.8429 (m-80) cc_final: 0.8110 (m-10) REVERT: A 484 GLU cc_start: 0.8311 (pp20) cc_final: 0.8095 (tm-30) REVERT: A 504 LEU cc_start: 0.8333 (mt) cc_final: 0.8122 (mt) REVERT: A 602 PHE cc_start: 0.8111 (p90) cc_final: 0.7395 (p90) REVERT: A 641 GLU cc_start: 0.8639 (pt0) cc_final: 0.8116 (pt0) REVERT: A 667 MET cc_start: 0.8639 (tpt) cc_final: 0.8126 (tpp) REVERT: A 697 ILE cc_start: 0.8958 (mt) cc_final: 0.8716 (mt) REVERT: A 702 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8823 (tp30) REVERT: A 707 HIS cc_start: 0.7630 (m90) cc_final: 0.6404 (m-70) REVERT: A 716 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8776 (mm-30) REVERT: A 754 MET cc_start: 0.9081 (tpt) cc_final: 0.8622 (tpt) REVERT: A 755 ASN cc_start: 0.9095 (m110) cc_final: 0.8821 (m110) REVERT: A 803 ARG cc_start: 0.8589 (mmt180) cc_final: 0.7695 (tpt170) REVERT: B 15 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7939 (mm-40) REVERT: B 55 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7836 (ttpp) REVERT: B 124 THR cc_start: 0.8776 (m) cc_final: 0.8411 (p) REVERT: C 35 MET cc_start: 0.8727 (mmm) cc_final: 0.8208 (mmm) REVERT: C 67 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7528 (mtp-110) REVERT: C 79 LEU cc_start: 0.8476 (tp) cc_final: 0.7668 (tp) REVERT: C 90 ASP cc_start: 0.7811 (p0) cc_final: 0.7287 (p0) REVERT: C 96 CYS cc_start: 0.5971 (t) cc_final: 0.3326 (t) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2122 time to fit residues: 52.2542 Evaluate side-chains 147 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN A 725 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6893 Z= 0.295 Angle : 0.640 7.975 9302 Z= 0.339 Chirality : 0.042 0.143 1029 Planarity : 0.005 0.081 1206 Dihedral : 5.130 21.821 938 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: -1.78 (0.28), residues: 836 helix: -0.21 (0.25), residues: 422 sheet: -2.03 (0.55), residues: 91 loop : -2.17 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 37 HIS 0.008 0.001 HIS A 492 PHE 0.021 0.002 PHE A 552 TYR 0.019 0.002 TYR A 192 ARG 0.008 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9344 (tp) cc_final: 0.8845 (mt) REVERT: A 344 HIS cc_start: 0.8480 (p-80) cc_final: 0.8234 (p-80) REVERT: A 392 TYR cc_start: 0.8566 (m-80) cc_final: 0.8302 (m-10) REVERT: A 484 GLU cc_start: 0.8409 (pp20) cc_final: 0.8116 (tm-30) REVERT: A 602 PHE cc_start: 0.8210 (p90) cc_final: 0.7381 (p90) REVERT: A 618 GLU cc_start: 0.8570 (pp20) cc_final: 0.8118 (pp20) REVERT: A 641 GLU cc_start: 0.8656 (pt0) cc_final: 0.8059 (pt0) REVERT: A 667 MET cc_start: 0.8650 (tpt) cc_final: 0.8168 (tpp) REVERT: A 697 ILE cc_start: 0.9018 (mt) cc_final: 0.8778 (mt) REVERT: A 702 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8736 (tp30) REVERT: A 707 HIS cc_start: 0.7494 (m90) cc_final: 0.5906 (m170) REVERT: A 755 ASN cc_start: 0.9129 (m110) cc_final: 0.8802 (m110) REVERT: A 803 ARG cc_start: 0.8477 (mmt180) cc_final: 0.7735 (tpt170) REVERT: B 32 ASP cc_start: 0.7606 (p0) cc_final: 0.7234 (p0) REVERT: B 98 CYS cc_start: 0.7621 (t) cc_final: 0.6865 (t) REVERT: B 124 THR cc_start: 0.8862 (m) cc_final: 0.8531 (p) REVERT: C 67 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7330 (mtp-110) REVERT: C 79 LEU cc_start: 0.8265 (tp) cc_final: 0.7852 (tp) REVERT: C 95 TYR cc_start: 0.8351 (m-80) cc_final: 0.7963 (m-80) REVERT: C 96 CYS cc_start: 0.5748 (t) cc_final: 0.4586 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2138 time to fit residues: 50.4817 Evaluate side-chains 137 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 GLN B 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6893 Z= 0.224 Angle : 0.581 5.796 9302 Z= 0.310 Chirality : 0.041 0.127 1029 Planarity : 0.005 0.056 1206 Dihedral : 4.851 23.711 938 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % 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: -1.36 (0.29), residues: 836 helix: 0.16 (0.25), residues: 422 sheet: -1.77 (0.55), residues: 91 loop : -2.01 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 37 HIS 0.004 0.001 HIS A 492 PHE 0.020 0.002 PHE A 552 TYR 0.017 0.002 TYR A 192 ARG 0.007 0.001 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9050 (tp) cc_final: 0.8798 (mt) REVERT: A 392 TYR cc_start: 0.8527 (m-80) cc_final: 0.8262 (m-10) REVERT: A 484 GLU cc_start: 0.8436 (pp20) cc_final: 0.8066 (tm-30) REVERT: A 602 PHE cc_start: 0.8081 (p90) cc_final: 0.7208 (p90) REVERT: A 618 GLU cc_start: 0.8603 (pp20) cc_final: 0.8113 (pp20) REVERT: A 641 GLU cc_start: 0.8716 (pt0) cc_final: 0.8147 (pt0) REVERT: A 667 MET cc_start: 0.8542 (tpt) cc_final: 0.8062 (tpp) REVERT: A 697 ILE cc_start: 0.9017 (mt) cc_final: 0.8787 (mt) REVERT: A 702 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8802 (tp30) REVERT: A 755 ASN cc_start: 0.9108 (m110) cc_final: 0.8759 (m110) REVERT: B 32 ASP cc_start: 0.7591 (p0) cc_final: 0.7371 (p0) REVERT: B 82 TYR cc_start: 0.6318 (m-10) cc_final: 0.5676 (m-10) REVERT: B 85 MET cc_start: 0.8692 (mtt) cc_final: 0.8080 (mtm) REVERT: B 124 THR cc_start: 0.8835 (m) cc_final: 0.8515 (p) REVERT: C 30 PHE cc_start: 0.8665 (t80) cc_final: 0.8229 (t80) REVERT: C 39 ARG cc_start: 0.6564 (ptp90) cc_final: 0.6294 (ptp-170) REVERT: C 67 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7170 (mtp-110) REVERT: C 79 LEU cc_start: 0.8223 (tp) cc_final: 0.7862 (tp) REVERT: C 82 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7669 (tp-100) REVERT: C 85 ARG cc_start: 0.7523 (tmm160) cc_final: 0.7291 (ptm-80) REVERT: C 96 CYS cc_start: 0.5694 (t) cc_final: 0.4751 (t) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2075 time to fit residues: 48.6389 Evaluate side-chains 142 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN C 53 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6893 Z= 0.327 Angle : 0.662 7.339 9302 Z= 0.349 Chirality : 0.043 0.128 1029 Planarity : 0.005 0.047 1206 Dihedral : 5.200 25.030 938 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -1.48 (0.29), residues: 836 helix: 0.03 (0.25), residues: 423 sheet: -1.87 (0.55), residues: 96 loop : -2.00 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 48 HIS 0.006 0.001 HIS A 492 PHE 0.025 0.002 PHE A 552 TYR 0.024 0.002 TYR A 630 ARG 0.005 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9105 (tp) cc_final: 0.8822 (mt) REVERT: A 484 GLU cc_start: 0.8472 (pp20) cc_final: 0.8081 (tm-30) REVERT: A 504 LEU cc_start: 0.8326 (mt) cc_final: 0.8049 (mt) REVERT: A 602 PHE cc_start: 0.8125 (p90) cc_final: 0.7109 (p90) REVERT: A 618 GLU cc_start: 0.8648 (pp20) cc_final: 0.8146 (pp20) REVERT: A 641 GLU cc_start: 0.8674 (pt0) cc_final: 0.8057 (pt0) REVERT: A 667 MET cc_start: 0.8582 (tpt) cc_final: 0.8086 (tpp) REVERT: A 702 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8766 (mm-30) REVERT: A 754 MET cc_start: 0.9114 (tpt) cc_final: 0.8530 (tpt) REVERT: A 803 ARG cc_start: 0.8300 (mmt180) cc_final: 0.7539 (tpt170) REVERT: B 85 MET cc_start: 0.8776 (mtt) cc_final: 0.8152 (mtm) REVERT: B 124 THR cc_start: 0.8963 (m) cc_final: 0.8692 (p) REVERT: C 35 MET cc_start: 0.8644 (mmm) cc_final: 0.8097 (mmm) REVERT: C 67 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7591 (mtp-110) REVERT: C 79 LEU cc_start: 0.7888 (tp) cc_final: 0.7543 (tp) REVERT: C 96 CYS cc_start: 0.4900 (t) cc_final: 0.3797 (t) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2104 time to fit residues: 47.7076 Evaluate side-chains 132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6893 Z= 0.195 Angle : 0.600 11.598 9302 Z= 0.313 Chirality : 0.041 0.139 1029 Planarity : 0.004 0.042 1206 Dihedral : 4.762 23.255 938 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.13 (0.29), residues: 836 helix: 0.31 (0.26), residues: 427 sheet: -1.75 (0.53), residues: 99 loop : -1.83 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 37 HIS 0.003 0.001 HIS A 492 PHE 0.020 0.001 PHE A 349 TYR 0.017 0.002 TYR A 192 ARG 0.005 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9037 (tp) cc_final: 0.8784 (mt) REVERT: A 602 PHE cc_start: 0.8095 (p90) cc_final: 0.7111 (p90) REVERT: A 618 GLU cc_start: 0.8646 (pp20) cc_final: 0.8174 (pp20) REVERT: A 641 GLU cc_start: 0.8687 (pt0) cc_final: 0.8175 (pt0) REVERT: A 667 MET cc_start: 0.8507 (tpt) cc_final: 0.8026 (tpp) REVERT: A 697 ILE cc_start: 0.8997 (mt) cc_final: 0.8723 (mt) REVERT: A 702 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8799 (tp30) REVERT: A 755 ASN cc_start: 0.9092 (m-40) cc_final: 0.8805 (m110) REVERT: A 803 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7484 (tpt170) REVERT: A 814 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 819 MET cc_start: 0.8321 (ptp) cc_final: 0.8068 (ptp) REVERT: B 38 TRP cc_start: 0.7279 (m100) cc_final: 0.6755 (m100) REVERT: B 85 MET cc_start: 0.8761 (mtt) cc_final: 0.8065 (mtm) REVERT: B 98 CYS cc_start: 0.7814 (t) cc_final: 0.5682 (t) REVERT: B 124 THR cc_start: 0.8863 (m) cc_final: 0.8594 (p) REVERT: C 30 PHE cc_start: 0.8645 (t80) cc_final: 0.8104 (t80) REVERT: C 35 MET cc_start: 0.8836 (mmm) cc_final: 0.8329 (mmm) REVERT: C 67 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7224 (mtp-110) REVERT: C 79 LEU cc_start: 0.8162 (tp) cc_final: 0.7722 (tp) REVERT: C 85 ARG cc_start: 0.7364 (ptm-80) cc_final: 0.7016 (ptm-80) REVERT: C 96 CYS cc_start: 0.5255 (t) cc_final: 0.4533 (t) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2104 time to fit residues: 50.0585 Evaluate side-chains 143 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6893 Z= 0.170 Angle : 0.591 7.079 9302 Z= 0.309 Chirality : 0.040 0.129 1029 Planarity : 0.004 0.041 1206 Dihedral : 4.544 22.259 938 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -0.99 (0.29), residues: 836 helix: 0.43 (0.26), residues: 427 sheet: -1.81 (0.53), residues: 99 loop : -1.74 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 37 HIS 0.003 0.001 HIS A 492 PHE 0.022 0.001 PHE A 712 TYR 0.015 0.001 TYR A 192 ARG 0.009 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.9175 (ttm) cc_final: 0.8852 (tmm) REVERT: A 293 LEU cc_start: 0.8981 (tp) cc_final: 0.8766 (mt) REVERT: A 392 TYR cc_start: 0.8545 (m-80) cc_final: 0.8227 (m-10) REVERT: A 570 CYS cc_start: 0.7863 (m) cc_final: 0.7309 (m) REVERT: A 602 PHE cc_start: 0.8105 (p90) cc_final: 0.7125 (p90) REVERT: A 618 GLU cc_start: 0.8651 (pp20) cc_final: 0.8187 (pp20) REVERT: A 641 GLU cc_start: 0.8718 (pt0) cc_final: 0.8157 (pt0) REVERT: A 667 MET cc_start: 0.8514 (tpt) cc_final: 0.8038 (tpp) REVERT: A 697 ILE cc_start: 0.8941 (mt) cc_final: 0.8708 (mt) REVERT: A 702 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8827 (tp30) REVERT: A 746 LEU cc_start: 0.9380 (mt) cc_final: 0.9027 (mt) REVERT: A 754 MET cc_start: 0.9106 (tpt) cc_final: 0.8888 (tpt) REVERT: A 755 ASN cc_start: 0.9165 (m-40) cc_final: 0.8816 (m110) REVERT: A 804 MET cc_start: 0.5154 (ptm) cc_final: 0.4791 (ppp) REVERT: A 814 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8739 (tm-30) REVERT: B 38 TRP cc_start: 0.7352 (m100) cc_final: 0.6825 (m100) REVERT: B 85 MET cc_start: 0.8714 (mtt) cc_final: 0.8456 (mtm) REVERT: B 98 CYS cc_start: 0.7902 (t) cc_final: 0.5834 (t) REVERT: B 124 THR cc_start: 0.8857 (m) cc_final: 0.8633 (p) REVERT: C 30 PHE cc_start: 0.8666 (t80) cc_final: 0.8046 (t80) REVERT: C 35 MET cc_start: 0.8723 (mmm) cc_final: 0.8127 (mmm) REVERT: C 79 LEU cc_start: 0.8179 (tp) cc_final: 0.7723 (tp) REVERT: C 85 ARG cc_start: 0.7501 (ptm-80) cc_final: 0.7289 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2038 time to fit residues: 49.2688 Evaluate side-chains 144 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.0050 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6893 Z= 0.192 Angle : 0.598 7.281 9302 Z= 0.313 Chirality : 0.041 0.132 1029 Planarity : 0.004 0.039 1206 Dihedral : 4.532 21.799 938 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.86 (0.29), residues: 836 helix: 0.52 (0.26), residues: 427 sheet: -1.65 (0.56), residues: 89 loop : -1.68 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 37 HIS 0.003 0.001 HIS A 492 PHE 0.022 0.002 PHE A 349 TYR 0.019 0.002 TYR A 761 ARG 0.007 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9009 (tp) cc_final: 0.8773 (mt) REVERT: A 392 TYR cc_start: 0.8566 (m-80) cc_final: 0.8244 (m-10) REVERT: A 570 CYS cc_start: 0.7788 (m) cc_final: 0.7333 (m) REVERT: A 618 GLU cc_start: 0.8671 (pp20) cc_final: 0.8193 (pp20) REVERT: A 641 GLU cc_start: 0.8642 (pt0) cc_final: 0.8140 (pt0) REVERT: A 667 MET cc_start: 0.8532 (tpt) cc_final: 0.8060 (tpp) REVERT: A 697 ILE cc_start: 0.8942 (mt) cc_final: 0.8710 (mt) REVERT: A 702 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8681 (tp30) REVERT: A 707 HIS cc_start: 0.7637 (m90) cc_final: 0.5790 (m170) REVERT: A 746 LEU cc_start: 0.9425 (mt) cc_final: 0.9052 (mt) REVERT: A 755 ASN cc_start: 0.9185 (m-40) cc_final: 0.8844 (m110) REVERT: A 803 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7388 (tpt170) REVERT: A 814 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8687 (tm-30) REVERT: B 38 TRP cc_start: 0.7367 (m100) cc_final: 0.6864 (m100) REVERT: B 85 MET cc_start: 0.8745 (mtt) cc_final: 0.8462 (mtm) REVERT: B 98 CYS cc_start: 0.7729 (t) cc_final: 0.5502 (t) REVERT: B 124 THR cc_start: 0.8876 (m) cc_final: 0.8654 (p) REVERT: C 30 PHE cc_start: 0.8627 (t80) cc_final: 0.8053 (t80) REVERT: C 79 LEU cc_start: 0.8166 (tp) cc_final: 0.7747 (tp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1855 time to fit residues: 43.6575 Evaluate side-chains 143 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 71 optimal weight: 0.0010 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6893 Z= 0.214 Angle : 0.618 7.409 9302 Z= 0.326 Chirality : 0.042 0.237 1029 Planarity : 0.004 0.038 1206 Dihedral : 4.650 21.970 938 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.84 (0.29), residues: 836 helix: 0.57 (0.26), residues: 423 sheet: -1.62 (0.55), residues: 89 loop : -1.71 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 37 HIS 0.004 0.001 HIS A 492 PHE 0.024 0.002 PHE A 712 TYR 0.022 0.002 TYR A 761 ARG 0.005 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9026 (tp) cc_final: 0.8791 (mt) REVERT: A 504 LEU cc_start: 0.8312 (mt) cc_final: 0.8110 (mt) REVERT: A 570 CYS cc_start: 0.7903 (m) cc_final: 0.7444 (m) REVERT: A 602 PHE cc_start: 0.8069 (p90) cc_final: 0.7038 (p90) REVERT: A 618 GLU cc_start: 0.8694 (pp20) cc_final: 0.8217 (pp20) REVERT: A 638 LYS cc_start: 0.8299 (mmtm) cc_final: 0.8088 (mmtp) REVERT: A 641 GLU cc_start: 0.8617 (pt0) cc_final: 0.8004 (pt0) REVERT: A 667 MET cc_start: 0.8542 (tpt) cc_final: 0.8076 (tpp) REVERT: A 697 ILE cc_start: 0.8952 (mt) cc_final: 0.8716 (mt) REVERT: A 702 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8511 (tp30) REVERT: A 707 HIS cc_start: 0.7659 (m90) cc_final: 0.6006 (m-70) REVERT: A 743 ARG cc_start: 0.8374 (mtt180) cc_final: 0.8134 (mtm-85) REVERT: A 754 MET cc_start: 0.9055 (tpt) cc_final: 0.8679 (tpt) REVERT: A 755 ASN cc_start: 0.9201 (m-40) cc_final: 0.8825 (m110) REVERT: A 803 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7297 (tpt170) REVERT: A 814 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8740 (tm-30) REVERT: B 38 TRP cc_start: 0.7374 (m100) cc_final: 0.6902 (m100) REVERT: B 85 MET cc_start: 0.8669 (mtt) cc_final: 0.8416 (mtm) REVERT: B 98 CYS cc_start: 0.7733 (t) cc_final: 0.5580 (t) REVERT: B 124 THR cc_start: 0.8877 (m) cc_final: 0.8659 (p) REVERT: C 30 PHE cc_start: 0.8663 (t80) cc_final: 0.8063 (t80) REVERT: C 79 LEU cc_start: 0.8216 (tp) cc_final: 0.7467 (tp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2002 time to fit residues: 46.7319 Evaluate side-chains 146 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 chunk 77 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6893 Z= 0.166 Angle : 0.607 7.789 9302 Z= 0.316 Chirality : 0.041 0.213 1029 Planarity : 0.004 0.039 1206 Dihedral : 4.479 22.030 938 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.65 (0.29), residues: 836 helix: 0.68 (0.26), residues: 423 sheet: -1.45 (0.56), residues: 87 loop : -1.57 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 37 HIS 0.003 0.001 HIS A 492 PHE 0.024 0.002 PHE A 349 TYR 0.022 0.002 TYR A 761 ARG 0.006 0.000 ARG C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8987 (tp) cc_final: 0.8738 (mt) REVERT: A 392 TYR cc_start: 0.8568 (m-80) cc_final: 0.8236 (m-10) REVERT: A 504 LEU cc_start: 0.8308 (mt) cc_final: 0.8099 (mt) REVERT: A 570 CYS cc_start: 0.7767 (m) cc_final: 0.7233 (m) REVERT: A 602 PHE cc_start: 0.8054 (p90) cc_final: 0.7015 (p90) REVERT: A 618 GLU cc_start: 0.8710 (pp20) cc_final: 0.8228 (pp20) REVERT: A 638 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7923 (mmmm) REVERT: A 641 GLU cc_start: 0.8573 (pt0) cc_final: 0.7968 (pt0) REVERT: A 667 MET cc_start: 0.8517 (tpt) cc_final: 0.8058 (tpp) REVERT: A 697 ILE cc_start: 0.8931 (mt) cc_final: 0.8693 (mt) REVERT: A 702 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8537 (tp30) REVERT: A 707 HIS cc_start: 0.7645 (m90) cc_final: 0.5984 (m-70) REVERT: A 743 ARG cc_start: 0.8296 (mtt180) cc_final: 0.8042 (mtm-85) REVERT: A 755 ASN cc_start: 0.9207 (m-40) cc_final: 0.8875 (m110) REVERT: A 803 ARG cc_start: 0.8087 (mmt180) cc_final: 0.7252 (tpt170) REVERT: A 804 MET cc_start: 0.5041 (ptm) cc_final: 0.4810 (ppp) REVERT: A 814 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8721 (tm-30) REVERT: B 38 TRP cc_start: 0.7365 (m100) cc_final: 0.6971 (m100) REVERT: B 85 MET cc_start: 0.8667 (mtt) cc_final: 0.8435 (mtm) REVERT: B 98 CYS cc_start: 0.7807 (t) cc_final: 0.5607 (t) REVERT: B 124 THR cc_start: 0.8843 (m) cc_final: 0.8629 (p) REVERT: C 30 PHE cc_start: 0.8669 (t80) cc_final: 0.8280 (t80) REVERT: C 79 LEU cc_start: 0.8132 (tp) cc_final: 0.7573 (tp) REVERT: C 96 CYS cc_start: 0.5708 (t) cc_final: 0.4740 (t) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1884 time to fit residues: 44.4718 Evaluate side-chains 148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.055889 restraints weight = 25123.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.057581 restraints weight = 16046.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.058766 restraints weight = 11821.919| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6893 Z= 0.311 Angle : 0.685 7.664 9302 Z= 0.362 Chirality : 0.044 0.131 1029 Planarity : 0.005 0.038 1206 Dihedral : 5.000 22.475 938 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.94 (0.29), residues: 836 helix: 0.38 (0.26), residues: 423 sheet: -1.39 (0.56), residues: 87 loop : -1.69 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 37 HIS 0.010 0.002 HIS A 358 PHE 0.031 0.002 PHE A 552 TYR 0.017 0.002 TYR A 761 ARG 0.004 0.000 ARG C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.51 seconds wall clock time: 36 minutes 18.90 seconds (2178.90 seconds total)