Starting phenix.real_space_refine on Mon Mar 11 03:08:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zox_14849/03_2024/7zox_14849.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zox_14849/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zox_14849/03_2024/7zox_14849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zox_14849/03_2024/7zox_14849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zox_14849/03_2024/7zox_14849.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zox_14849/03_2024/7zox_14849.pdb" } 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 Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A GLU 573": "OE1" <-> "OE2" Residue "A PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A ASP 605": "OD1" <-> "OD2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A ASP 713": "OD1" <-> "OD2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ASP 726": "OD1" <-> "OD2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "C ASP 90": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.49, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 2.83 Conformation dependent library (CDL) restraints added in 1.3 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: 0.61 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: 2.22 Time building geometry restraints manager: 3.09 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: 99.64 - 106.52: 144 106.52 - 113.40: 3757 113.40 - 120.27: 2508 120.27 - 127.15: 2846 127.15 - 134.02: 47 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 2.520 nonbonded pdb=" O GLN A 653 " pdb=" NH1 ARG A 661 " model vdw 2.221 2.520 nonbonded pdb=" O ASP A 781 " pdb=" OG SER A 784 " model vdw 2.236 2.440 nonbonded pdb=" OG SER A 724 " pdb=" OD1 ASP A 726 " model vdw 2.238 2.440 nonbonded pdb=" O ASN C 53 " pdb=" NH1 ARG C 72 " model vdw 2.240 2.520 ... (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 ========== 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: 2.280 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: 5.260 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.260 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.310 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 0.842 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: 0.2315 time to fit residues: 57.0064 Evaluate side-chains 143 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 528 ASN A 745 ASN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 79 ASN C 53 ASN C 77 ASN C 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1925 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= 0.221 Angle : 0.580 5.548 9302 Z= 0.311 Chirality : 0.040 0.140 1029 Planarity : 0.004 0.052 1206 Dihedral : 5.125 22.677 938 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % 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: -2.48 (0.27), residues: 836 helix: -0.80 (0.23), residues: 418 sheet: -2.61 (0.49), residues: 96 loop : -2.34 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 37 HIS 0.004 0.001 HIS A 492 PHE 0.019 0.001 PHE A 796 TYR 0.027 0.002 TYR A 262 ARG 0.006 0.001 ARG A 377 *********************** 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 179 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.859 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: 0.9297 (tp) cc_final: 0.8820 (mt) REVERT: A 320 TRP cc_start: 0.8114 (m100) cc_final: 0.7099 (m100) REVERT: A 344 HIS cc_start: 0.8556 (p-80) cc_final: 0.8340 (p-80) REVERT: A 349 PHE cc_start: 0.8722 (t80) cc_final: 0.8477 (t80) REVERT: A 392 TYR cc_start: 0.8447 (m-80) cc_final: 0.8104 (m-10) REVERT: A 504 LEU cc_start: 0.8335 (mt) cc_final: 0.8107 (mt) REVERT: A 602 PHE cc_start: 0.8132 (p90) cc_final: 0.7373 (p90) REVERT: A 641 GLU cc_start: 0.8625 (pt0) cc_final: 0.8111 (pt0) REVERT: A 667 MET cc_start: 0.8634 (tpt) cc_final: 0.8140 (tpp) REVERT: A 697 ILE cc_start: 0.8956 (mt) cc_final: 0.8714 (mt) REVERT: A 702 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8437 (tp30) REVERT: A 707 HIS cc_start: 0.7635 (m90) cc_final: 0.5835 (m-70) REVERT: A 716 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8774 (mm-30) REVERT: A 754 MET cc_start: 0.9076 (tpt) cc_final: 0.8536 (tpt) REVERT: A 803 ARG cc_start: 0.8652 (mmt180) cc_final: 0.7761 (tpt170) REVERT: B 15 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7999 (mm-40) REVERT: B 55 LYS cc_start: 0.7995 (ptmm) cc_final: 0.7732 (ttpp) REVERT: B 82 TYR cc_start: 0.6516 (m-10) cc_final: 0.6179 (m-10) REVERT: B 98 CYS cc_start: 0.7672 (t) cc_final: 0.6914 (t) REVERT: B 124 THR cc_start: 0.8818 (m) cc_final: 0.8474 (p) REVERT: C 37 TRP cc_start: 0.7162 (m100) cc_final: 0.6781 (m100) REVERT: C 67 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7218 (mtp-110) REVERT: C 79 LEU cc_start: 0.8477 (tp) cc_final: 0.7730 (tp) REVERT: C 96 CYS cc_start: 0.5913 (t) cc_final: 0.3078 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1833 time to fit residues: 43.5932 Evaluate side-chains 139 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 0.0570 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 457 ASN A 725 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6893 Z= 0.264 Angle : 0.602 5.717 9302 Z= 0.319 Chirality : 0.041 0.130 1029 Planarity : 0.004 0.048 1206 Dihedral : 5.093 21.683 938 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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: -1.78 (0.28), residues: 836 helix: -0.21 (0.25), residues: 421 sheet: -2.22 (0.53), residues: 96 loop : -2.07 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 37 HIS 0.008 0.001 HIS A 492 PHE 0.020 0.002 PHE A 552 TYR 0.018 0.002 TYR A 192 ARG 0.005 0.000 ARG C 20 *********************** 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 180 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.848 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: symmetry clash REVERT: A 293 LEU cc_start: 0.9316 (tp) cc_final: 0.8833 (mt) REVERT: A 320 TRP cc_start: 0.8089 (m100) cc_final: 0.7169 (m100) REVERT: A 344 HIS cc_start: 0.8556 (p-80) cc_final: 0.8321 (p-80) REVERT: A 349 PHE cc_start: 0.8708 (t80) cc_final: 0.8470 (t80) REVERT: A 504 LEU cc_start: 0.8396 (mt) cc_final: 0.8177 (mt) REVERT: A 570 CYS cc_start: 0.7922 (m) cc_final: 0.7625 (m) REVERT: A 618 GLU cc_start: 0.8525 (pp20) cc_final: 0.8100 (pp20) REVERT: A 641 GLU cc_start: 0.8671 (pt0) cc_final: 0.8049 (pt0) REVERT: A 667 MET cc_start: 0.8610 (tpt) cc_final: 0.8138 (tpp) REVERT: A 702 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8397 (tp30) REVERT: A 707 HIS cc_start: 0.7562 (m90) cc_final: 0.5670 (m-70) REVERT: A 755 ASN cc_start: 0.9112 (m110) cc_final: 0.8882 (m110) REVERT: A 803 ARG cc_start: 0.8599 (mmt180) cc_final: 0.7686 (tpt170) REVERT: B 124 THR cc_start: 0.8860 (m) cc_final: 0.8546 (p) REVERT: C 35 MET cc_start: 0.8599 (mmm) cc_final: 0.8046 (mmm) REVERT: C 67 ARG cc_start: 0.7547 (mtm110) cc_final: 0.7151 (mtp-110) REVERT: C 90 ASP cc_start: 0.7543 (p0) cc_final: 0.6989 (p0) REVERT: C 95 TYR cc_start: 0.8313 (m-80) cc_final: 0.8024 (m-10) REVERT: C 99 MET cc_start: 0.8087 (tmm) cc_final: 0.7780 (tmm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1997 time to fit residues: 46.9154 Evaluate side-chains 136 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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: 10.0000 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 0.0170 overall best weight: 1.0622 ------------------------------------------------------------------------------- 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 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS A 814 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2792 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= 0.179 Angle : 0.546 6.014 9302 Z= 0.291 Chirality : 0.040 0.129 1029 Planarity : 0.004 0.045 1206 Dihedral : 4.693 22.336 938 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -1.24 (0.29), residues: 836 helix: 0.22 (0.26), residues: 427 sheet: -1.87 (0.54), residues: 91 loop : -1.87 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 37 HIS 0.002 0.001 HIS A 492 PHE 0.017 0.001 PHE A 552 TYR 0.018 0.002 TYR A 324 ARG 0.006 0.000 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 181 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.865 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: 0.9000 (tp) cc_final: 0.8769 (mt) REVERT: A 320 TRP cc_start: 0.8021 (m100) cc_final: 0.6960 (m100) REVERT: A 392 TYR cc_start: 0.8584 (m-80) cc_final: 0.7887 (m-10) REVERT: A 570 CYS cc_start: 0.7908 (m) cc_final: 0.7439 (m) REVERT: A 602 PHE cc_start: 0.8306 (p90) cc_final: 0.7402 (p90) REVERT: A 618 GLU cc_start: 0.8583 (pp20) cc_final: 0.8158 (pp20) REVERT: A 641 GLU cc_start: 0.8650 (pt0) cc_final: 0.8095 (pt0) REVERT: A 667 MET cc_start: 0.8556 (tpt) cc_final: 0.8074 (tpp) REVERT: A 697 ILE cc_start: 0.8957 (mt) cc_final: 0.8734 (mt) REVERT: A 702 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8701 (tp30) REVERT: A 703 TYR cc_start: 0.8955 (t80) cc_final: 0.8378 (t80) REVERT: A 707 HIS cc_start: 0.7585 (m90) cc_final: 0.5632 (m170) REVERT: A 755 ASN cc_start: 0.9112 (m110) cc_final: 0.8753 (m110) REVERT: A 803 ARG cc_start: 0.8534 (mmt180) cc_final: 0.7703 (tpt170) REVERT: B 38 TRP cc_start: 0.7324 (m100) cc_final: 0.6699 (m100) REVERT: B 98 CYS cc_start: 0.7798 (t) cc_final: 0.5860 (t) REVERT: B 124 THR cc_start: 0.8768 (m) cc_final: 0.8493 (p) REVERT: C 30 PHE cc_start: 0.8719 (t80) cc_final: 0.8295 (t80) REVERT: C 35 MET cc_start: 0.8705 (mmm) cc_final: 0.8237 (mmm) REVERT: C 37 TRP cc_start: 0.7028 (m100) cc_final: 0.6691 (m100) REVERT: C 67 ARG cc_start: 0.7549 (mtm110) cc_final: 0.7171 (mtp-110) REVERT: C 79 LEU cc_start: 0.8343 (tp) cc_final: 0.7526 (tp) REVERT: C 85 ARG cc_start: 0.7371 (ppt170) cc_final: 0.7152 (ptm-80) REVERT: C 94 TYR cc_start: 0.7934 (m-80) cc_final: 0.7479 (m-80) REVERT: C 95 TYR cc_start: 0.8385 (m-80) cc_final: 0.8068 (m-80) REVERT: C 96 CYS cc_start: 0.5459 (t) cc_final: 0.3154 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1859 time to fit residues: 44.4953 Evaluate side-chains 147 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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: 8.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 619 ASN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN C 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2743 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= 0.346 Angle : 0.663 7.609 9302 Z= 0.350 Chirality : 0.043 0.126 1029 Planarity : 0.005 0.047 1206 Dihedral : 5.191 22.676 938 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % 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: -1.47 (0.29), residues: 836 helix: -0.02 (0.25), residues: 421 sheet: -1.92 (0.55), residues: 91 loop : -1.90 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 48 HIS 0.008 0.001 HIS A 492 PHE 0.025 0.003 PHE A 552 TYR 0.019 0.002 TYR A 630 ARG 0.003 0.000 ARG C 20 *********************** 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 166 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.777 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: symmetry clash REVERT: A 293 LEU cc_start: 0.9070 (tp) cc_final: 0.8844 (mt) REVERT: A 320 TRP cc_start: 0.8069 (m100) cc_final: 0.7201 (m100) REVERT: A 504 LEU cc_start: 0.8306 (mt) cc_final: 0.8029 (mt) REVERT: A 570 CYS cc_start: 0.8034 (m) cc_final: 0.7826 (m) REVERT: A 602 PHE cc_start: 0.8288 (p90) cc_final: 0.7301 (p90) REVERT: A 618 GLU cc_start: 0.8560 (pp20) cc_final: 0.8141 (pp20) REVERT: A 630 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: A 641 GLU cc_start: 0.8642 (pt0) cc_final: 0.8023 (pt0) REVERT: A 667 MET cc_start: 0.8598 (tpt) cc_final: 0.8108 (tpp) REVERT: A 702 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8746 (mm-30) REVERT: A 754 MET cc_start: 0.9123 (tpt) cc_final: 0.8693 (tpt) REVERT: A 755 ASN cc_start: 0.9174 (m110) cc_final: 0.8870 (m110) REVERT: A 803 ARG cc_start: 0.8655 (mmt180) cc_final: 0.7868 (tpt170) REVERT: A 814 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8681 (tm-30) REVERT: B 85 MET cc_start: 0.8754 (mtt) cc_final: 0.8048 (mtm) REVERT: B 124 THR cc_start: 0.8906 (m) cc_final: 0.8662 (p) REVERT: C 37 TRP cc_start: 0.7080 (m100) cc_final: 0.6781 (m100) REVERT: C 67 ARG cc_start: 0.7708 (mtm110) cc_final: 0.7380 (mtp-110) REVERT: C 79 LEU cc_start: 0.8400 (tp) cc_final: 0.7938 (tp) REVERT: C 83 MET cc_start: 0.7413 (ptt) cc_final: 0.7002 (mtt) REVERT: C 90 ASP cc_start: 0.7366 (p0) cc_final: 0.6790 (p0) REVERT: C 96 CYS cc_start: 0.5546 (t) cc_final: 0.3674 (t) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1871 time to fit residues: 41.1541 Evaluate side-chains 136 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 0.5980 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 403 ASN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN C 82 GLN C 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3188 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 : 0.573 10.428 9302 Z= 0.297 Chirality : 0.040 0.150 1029 Planarity : 0.004 0.042 1206 Dihedral : 4.568 21.243 938 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.29), residues: 836 helix: 0.36 (0.26), residues: 427 sheet: -1.84 (0.55), residues: 91 loop : -1.70 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 48 HIS 0.002 0.000 HIS A 492 PHE 0.022 0.001 PHE A 349 TYR 0.016 0.002 TYR A 324 ARG 0.004 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 184 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.810 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 183 MET cc_start: 0.7995 (tmm) cc_final: 0.7754 (tmm) REVERT: A 293 LEU cc_start: 0.9001 (tp) cc_final: 0.8757 (mt) REVERT: A 320 TRP cc_start: 0.7988 (m100) cc_final: 0.7096 (m100) REVERT: A 392 TYR cc_start: 0.8562 (m-80) cc_final: 0.8333 (m-10) REVERT: A 570 CYS cc_start: 0.7782 (m) cc_final: 0.7284 (m) REVERT: A 602 PHE cc_start: 0.8260 (p90) cc_final: 0.7225 (p90) REVERT: A 618 GLU cc_start: 0.8553 (pp20) cc_final: 0.8104 (pp20) REVERT: A 641 GLU cc_start: 0.8662 (pt0) cc_final: 0.8097 (pt0) REVERT: A 667 MET cc_start: 0.8507 (tpt) cc_final: 0.8035 (tpp) REVERT: A 697 ILE cc_start: 0.9001 (mt) cc_final: 0.8715 (mt) REVERT: A 702 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8409 (tp30) REVERT: A 703 TYR cc_start: 0.8923 (t80) cc_final: 0.8170 (t80) REVERT: A 707 HIS cc_start: 0.7611 (m90) cc_final: 0.5659 (m-70) REVERT: A 755 ASN cc_start: 0.9110 (m110) cc_final: 0.8773 (m110) REVERT: A 803 ARG cc_start: 0.8511 (mmt180) cc_final: 0.7731 (tpt170) REVERT: A 814 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8694 (tm-30) REVERT: B 38 TRP cc_start: 0.7249 (m100) cc_final: 0.6729 (m100) REVERT: B 98 CYS cc_start: 0.7861 (t) cc_final: 0.5905 (t) REVERT: B 124 THR cc_start: 0.8773 (m) cc_final: 0.8516 (p) REVERT: C 30 PHE cc_start: 0.8735 (t80) cc_final: 0.8422 (t80) REVERT: C 37 TRP cc_start: 0.7062 (m100) cc_final: 0.6598 (m100) REVERT: C 67 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7385 (mtp-110) REVERT: C 79 LEU cc_start: 0.8328 (tp) cc_final: 0.7466 (tp) REVERT: C 94 TYR cc_start: 0.7938 (m-80) cc_final: 0.7738 (m-80) REVERT: C 96 CYS cc_start: 0.5555 (t) cc_final: 0.2857 (t) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2025 time to fit residues: 48.3032 Evaluate side-chains 143 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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: 0.7980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 489 HIS A 550 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3500 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= 0.171 Angle : 0.575 7.034 9302 Z= 0.301 Chirality : 0.041 0.274 1029 Planarity : 0.004 0.046 1206 Dihedral : 4.446 19.825 938 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.81 (0.29), residues: 836 helix: 0.54 (0.26), residues: 427 sheet: -1.72 (0.57), residues: 89 loop : -1.60 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 48 HIS 0.003 0.001 HIS A 492 PHE 0.022 0.002 PHE A 712 TYR 0.024 0.002 TYR A 630 ARG 0.005 0.000 ARG C 20 *********************** 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 182 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.877 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: 0.8984 (tp) cc_final: 0.8733 (mt) REVERT: A 320 TRP cc_start: 0.8037 (m100) cc_final: 0.6982 (m100) REVERT: A 392 TYR cc_start: 0.8582 (m-80) cc_final: 0.7919 (m-10) REVERT: A 504 LEU cc_start: 0.8305 (mt) cc_final: 0.8096 (mt) REVERT: A 570 CYS cc_start: 0.7784 (m) cc_final: 0.7114 (m) REVERT: A 602 PHE cc_start: 0.8320 (p90) cc_final: 0.7127 (p90) REVERT: A 618 GLU cc_start: 0.8596 (pp20) cc_final: 0.8142 (pp20) REVERT: A 638 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7879 (mmmm) REVERT: A 641 GLU cc_start: 0.8603 (pt0) cc_final: 0.8076 (pt0) REVERT: A 667 MET cc_start: 0.8539 (tpt) cc_final: 0.8090 (tpp) REVERT: A 697 ILE cc_start: 0.8964 (mt) cc_final: 0.8705 (mt) REVERT: A 702 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8714 (tp30) REVERT: A 707 HIS cc_start: 0.7607 (m90) cc_final: 0.5611 (m170) REVERT: A 754 MET cc_start: 0.9008 (tpt) cc_final: 0.8604 (tpt) REVERT: A 755 ASN cc_start: 0.9072 (m110) cc_final: 0.8847 (m110) REVERT: A 814 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8716 (tm-30) REVERT: B 38 TRP cc_start: 0.7305 (m100) cc_final: 0.7068 (m100) REVERT: B 85 MET cc_start: 0.8774 (mtt) cc_final: 0.8567 (mtm) REVERT: B 98 CYS cc_start: 0.7855 (t) cc_final: 0.5650 (t) REVERT: B 124 THR cc_start: 0.8839 (m) cc_final: 0.8623 (p) REVERT: C 30 PHE cc_start: 0.8701 (t80) cc_final: 0.7773 (t80) REVERT: C 35 MET cc_start: 0.8611 (mmm) cc_final: 0.8083 (mmm) REVERT: C 37 TRP cc_start: 0.6875 (m100) cc_final: 0.6498 (m100) REVERT: C 67 ARG cc_start: 0.7582 (mtm110) cc_final: 0.7316 (mtp-110) REVERT: C 79 LEU cc_start: 0.8324 (tp) cc_final: 0.7480 (tp) REVERT: C 94 TYR cc_start: 0.7494 (m-80) cc_final: 0.7219 (m-80) REVERT: C 96 CYS cc_start: 0.5360 (t) cc_final: 0.3174 (t) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1943 time to fit residues: 46.0725 Evaluate side-chains 141 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7977 moved from start: 0.3649 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= 0.183 Angle : 0.591 7.196 9302 Z= 0.310 Chirality : 0.041 0.187 1029 Planarity : 0.004 0.040 1206 Dihedral : 4.532 19.394 938 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -0.73 (0.29), residues: 836 helix: 0.63 (0.26), residues: 417 sheet: -1.66 (0.55), residues: 89 loop : -1.55 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 48 HIS 0.003 0.001 HIS A 492 PHE 0.022 0.002 PHE A 349 TYR 0.021 0.002 TYR A 630 ARG 0.004 0.000 ARG C 20 *********************** 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 180 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.844 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: 0.8981 (tp) cc_final: 0.8733 (mt) REVERT: A 320 TRP cc_start: 0.8038 (m100) cc_final: 0.7021 (m100) REVERT: A 392 TYR cc_start: 0.8551 (m-80) cc_final: 0.7880 (m-10) REVERT: A 504 LEU cc_start: 0.8286 (mt) cc_final: 0.8004 (mt) REVERT: A 570 CYS cc_start: 0.7930 (m) cc_final: 0.6693 (m) REVERT: A 602 PHE cc_start: 0.8213 (p90) cc_final: 0.7053 (p90) REVERT: A 618 GLU cc_start: 0.8588 (pp20) cc_final: 0.8099 (pp20) REVERT: A 638 LYS cc_start: 0.8214 (mmtp) cc_final: 0.7897 (mmmm) REVERT: A 641 GLU cc_start: 0.8607 (pt0) cc_final: 0.8080 (pt0) REVERT: A 667 MET cc_start: 0.8527 (tpt) cc_final: 0.8040 (tpp) REVERT: A 697 ILE cc_start: 0.8936 (mt) cc_final: 0.8706 (mt) REVERT: A 702 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8700 (mm-30) REVERT: A 703 TYR cc_start: 0.8592 (t80) cc_final: 0.8119 (t80) REVERT: A 754 MET cc_start: 0.8999 (tpt) cc_final: 0.8647 (tpt) REVERT: A 755 ASN cc_start: 0.9104 (m110) cc_final: 0.8797 (m110) REVERT: A 803 ARG cc_start: 0.8201 (mmt180) cc_final: 0.7508 (tpt170) REVERT: A 814 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8786 (tm-30) REVERT: B 38 TRP cc_start: 0.7293 (m100) cc_final: 0.6934 (m100) REVERT: B 48 GLU cc_start: 0.6106 (mt-10) cc_final: 0.5850 (mt-10) REVERT: B 98 CYS cc_start: 0.7598 (t) cc_final: 0.5702 (t) REVERT: B 124 THR cc_start: 0.8870 (m) cc_final: 0.8647 (p) REVERT: C 30 PHE cc_start: 0.8632 (t80) cc_final: 0.8221 (t80) REVERT: C 35 MET cc_start: 0.8623 (mmm) cc_final: 0.8132 (mmm) REVERT: C 37 TRP cc_start: 0.6857 (m100) cc_final: 0.6444 (m100) REVERT: C 67 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7298 (mtp-110) REVERT: C 73 ASP cc_start: 0.8514 (t70) cc_final: 0.8274 (t0) REVERT: C 79 LEU cc_start: 0.8319 (tp) cc_final: 0.7390 (tp) REVERT: C 96 CYS cc_start: 0.5343 (t) cc_final: 0.3144 (t) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2041 time to fit residues: 47.9459 Evaluate side-chains 145 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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: 0.4980 chunk 77 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 421 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: 0.7981 moved from start: 0.3746 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= 0.183 Angle : 0.580 7.049 9302 Z= 0.304 Chirality : 0.041 0.180 1029 Planarity : 0.004 0.039 1206 Dihedral : 4.489 19.650 938 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -0.66 (0.29), residues: 836 helix: 0.64 (0.26), residues: 423 sheet: -1.48 (0.57), residues: 83 loop : -1.53 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 48 HIS 0.003 0.001 HIS A 492 PHE 0.025 0.002 PHE A 712 TYR 0.021 0.002 TYR A 761 ARG 0.004 0.000 ARG C 20 *********************** 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 fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.873 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: 0.8961 (tp) cc_final: 0.8738 (mt) REVERT: A 320 TRP cc_start: 0.8038 (m100) cc_final: 0.7010 (m100) REVERT: A 392 TYR cc_start: 0.8541 (m-80) cc_final: 0.7880 (m-10) REVERT: A 504 LEU cc_start: 0.8280 (mt) cc_final: 0.8008 (mt) REVERT: A 570 CYS cc_start: 0.7645 (m) cc_final: 0.7246 (m) REVERT: A 618 GLU cc_start: 0.8523 (pp20) cc_final: 0.8036 (pp20) REVERT: A 638 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7873 (mmmm) REVERT: A 641 GLU cc_start: 0.8619 (pt0) cc_final: 0.8064 (pt0) REVERT: A 667 MET cc_start: 0.8511 (tpt) cc_final: 0.8048 (tpp) REVERT: A 697 ILE cc_start: 0.8952 (mt) cc_final: 0.8722 (mt) REVERT: A 702 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8743 (mm-30) REVERT: A 703 TYR cc_start: 0.8569 (t80) cc_final: 0.8114 (t80) REVERT: A 755 ASN cc_start: 0.9143 (m110) cc_final: 0.8825 (m110) REVERT: A 803 ARG cc_start: 0.8158 (mmt180) cc_final: 0.7429 (tpt170) REVERT: A 814 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8754 (tm-30) REVERT: B 38 TRP cc_start: 0.7293 (m100) cc_final: 0.6923 (m100) REVERT: B 48 GLU cc_start: 0.6101 (mt-10) cc_final: 0.5864 (mt-10) REVERT: B 98 CYS cc_start: 0.7575 (t) cc_final: 0.5695 (t) REVERT: B 124 THR cc_start: 0.8877 (m) cc_final: 0.8673 (p) REVERT: C 30 PHE cc_start: 0.8824 (t80) cc_final: 0.8268 (t80) REVERT: C 35 MET cc_start: 0.8637 (mmm) cc_final: 0.8140 (mmm) REVERT: C 37 TRP cc_start: 0.6818 (m100) cc_final: 0.6452 (m100) REVERT: C 67 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7280 (mtp-110) REVERT: C 79 LEU cc_start: 0.8243 (tp) cc_final: 0.7227 (tp) REVERT: C 96 CYS cc_start: 0.5279 (t) cc_final: 0.2998 (t) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1918 time to fit residues: 44.3419 Evaluate side-chains 140 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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: 0.7980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 52 optimal weight: 0.0000 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- 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 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6893 Z= 0.148 Angle : 0.577 7.823 9302 Z= 0.300 Chirality : 0.040 0.151 1029 Planarity : 0.004 0.040 1206 Dihedral : 4.285 18.929 938 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.60 (0.29), residues: 836 helix: 0.75 (0.26), residues: 416 sheet: -1.48 (0.53), residues: 94 loop : -1.52 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 48 HIS 0.013 0.001 HIS A 358 PHE 0.024 0.001 PHE A 349 TYR 0.023 0.001 TYR A 761 ARG 0.004 0.000 ARG C 20 ********************** 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 181 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.726 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: 0.8956 (tp) cc_final: 0.8709 (mt) REVERT: A 320 TRP cc_start: 0.7982 (m100) cc_final: 0.6979 (m100) REVERT: A 392 TYR cc_start: 0.8560 (m-80) cc_final: 0.7913 (m-10) REVERT: A 570 CYS cc_start: 0.7834 (m) cc_final: 0.7261 (m) REVERT: A 602 PHE cc_start: 0.8169 (p90) cc_final: 0.7026 (p90) REVERT: A 618 GLU cc_start: 0.8566 (pp20) cc_final: 0.8105 (pp20) REVERT: A 641 GLU cc_start: 0.8568 (pt0) cc_final: 0.8075 (pt0) REVERT: A 667 MET cc_start: 0.8486 (tpt) cc_final: 0.8022 (tpp) REVERT: A 697 ILE cc_start: 0.8951 (mt) cc_final: 0.8731 (mt) REVERT: A 702 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8677 (tp30) REVERT: A 707 HIS cc_start: 0.7578 (m90) cc_final: 0.5791 (m-70) REVERT: A 755 ASN cc_start: 0.9135 (m110) cc_final: 0.8915 (m110) REVERT: A 803 ARG cc_start: 0.8100 (mmt180) cc_final: 0.7458 (tpt170) REVERT: A 814 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8760 (tm-30) REVERT: A 819 MET cc_start: 0.7865 (ptp) cc_final: 0.7568 (ptm) REVERT: B 38 TRP cc_start: 0.7325 (m100) cc_final: 0.6961 (m100) REVERT: B 85 MET cc_start: 0.8691 (mtt) cc_final: 0.8299 (mmt) REVERT: B 98 CYS cc_start: 0.7580 (t) cc_final: 0.5601 (t) REVERT: B 124 THR cc_start: 0.8880 (m) cc_final: 0.8641 (p) REVERT: C 30 PHE cc_start: 0.8769 (t80) cc_final: 0.8246 (t80) REVERT: C 37 TRP cc_start: 0.6815 (m100) cc_final: 0.6607 (m100) REVERT: C 67 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7270 (mtp-110) REVERT: C 79 LEU cc_start: 0.8191 (tp) cc_final: 0.7127 (tp) REVERT: C 96 CYS cc_start: 0.5178 (t) cc_final: 0.2752 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1965 time to fit residues: 46.8223 Evaluate side-chains 143 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 12 optimal weight: 0.0370 chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.4870 ------------------------------------------------------------------------------- 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 421 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.060229 restraints weight = 24744.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061941 restraints weight = 16285.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.063158 restraints weight = 12157.685| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6893 Z= 0.150 Angle : 0.589 10.769 9302 Z= 0.305 Chirality : 0.041 0.213 1029 Planarity : 0.004 0.039 1206 Dihedral : 4.245 18.084 938 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -0.58 (0.29), residues: 836 helix: 0.81 (0.26), residues: 422 sheet: -1.50 (0.51), residues: 94 loop : -1.62 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 48 HIS 0.010 0.001 HIS A 358 PHE 0.027 0.002 PHE A 712 TYR 0.018 0.001 TYR A 630 ARG 0.004 0.000 ARG C 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.21 seconds wall clock time: 37 minutes 33.23 seconds (2253.23 seconds total)