Starting phenix.real_space_refine on Fri Mar 15 07:20:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/03_2024/7k8a_22724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/03_2024/7k8a_22724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/03_2024/7k8a_22724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/03_2024/7k8a_22724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/03_2024/7k8a_22724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/03_2024/7k8a_22724.pdb" } resolution = 3.65 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 ------------------------------------------------------------------------------- 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= 0.181 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5513 atoms to isotropic. 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 28 5.16 5 C 3570 2.51 5 N 913 2.21 5 O 1002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 5513 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5513 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 37, 'TRANS': 685} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.69, per 1000 atoms: 0.67 Number of scatterers: 5513 At special positions: 0 Unit cell: (92.22, 99.64, 100.7, 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 28 16.00 O 1002 8.00 N 913 7.00 C 3570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.09 Conformation dependent library (CDL) restraints added in 963.1 milliseconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 71.1% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.661A pdb=" N TRP A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 12 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 31 removed outlier: 4.589A pdb=" N VAL A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 48 through 62 removed outlier: 3.914A pdb=" N ALA A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 4.347A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 68 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 68' Processing helix chain 'A' and resid 83 through 101 removed outlier: 4.169A pdb=" N GLN A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 160 removed outlier: 3.566A pdb=" N ILE A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 170 through 206 removed outlier: 3.734A pdb=" N LEU A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 207 through 233 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 241 through 271 removed outlier: 3.529A pdb=" N VAL A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.774A pdb=" N SER A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 342 removed outlier: 4.998A pdb=" N ALA A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 removed outlier: 4.254A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 415 Proline residue: A 407 - end of helix removed outlier: 3.678A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 471 through 483 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.503A pdb=" N LYS A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 563 Processing helix chain 'A' and resid 563 through 583 removed outlier: 3.530A pdb=" N MET A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 612 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 630 through 660 removed outlier: 3.536A pdb=" N PHE A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 692 removed outlier: 4.275A pdb=" N ALA A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 722 removed outlier: 3.791A pdb=" N ILE A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.624A pdb=" N TRP A 737 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 747 removed outlier: 4.402A pdb=" N VAL A 745 " --> pdb=" O TRP A 741 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 removed outlier: 3.967A pdb=" N THR A 133 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 516 through 518 removed outlier: 3.523A pdb=" N ILE A 516 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 518 " --> pdb=" O LEU A 457 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1053 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: 1.70 Time building geometry restraints manager: 2.30 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: 1661 1.34 - 1.46: 864 1.46 - 1.58: 3045 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 5624 Sorted by residual: bond pdb=" N ASP A 78 " pdb=" CA ASP A 78 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.33e-02 5.65e+03 1.16e+01 bond pdb=" CA THR A 74 " pdb=" C THR A 74 " ideal model delta sigma weight residual 1.519 1.558 -0.039 1.28e-02 6.10e+03 9.24e+00 bond pdb=" CA ASP A 78 " pdb=" C ASP A 78 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.43e-02 4.89e+03 8.40e+00 bond pdb=" C THR A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.38e+00 bond pdb=" C VAL A 302 " pdb=" N PRO A 303 " ideal model delta sigma weight residual 1.337 1.361 -0.024 1.11e-02 8.12e+03 4.82e+00 ... (remaining 5619 not shown) Histogram of bond angle deviations from ideal: 98.72 - 106.18: 167 106.18 - 113.64: 3219 113.64 - 121.10: 2865 121.10 - 128.56: 1356 128.56 - 136.02: 46 Bond angle restraints: 7653 Sorted by residual: angle pdb=" N PRO A 75 " pdb=" CA PRO A 75 " pdb=" C PRO A 75 " ideal model delta sigma weight residual 110.70 117.53 -6.83 1.22e+00 6.72e-01 3.13e+01 angle pdb=" N LEU A 73 " pdb=" CA LEU A 73 " pdb=" C LEU A 73 " ideal model delta sigma weight residual 109.46 116.61 -7.15 1.66e+00 3.63e-01 1.86e+01 angle pdb=" C PRO A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 119.84 114.51 5.33 1.25e+00 6.40e-01 1.82e+01 angle pdb=" C ILE A 719 " pdb=" N ARG A 720 " pdb=" CA ARG A 720 " ideal model delta sigma weight residual 122.38 115.10 7.28 1.81e+00 3.05e-01 1.62e+01 angle pdb=" N PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta sigma weight residual 110.28 116.18 -5.90 1.55e+00 4.16e-01 1.45e+01 ... (remaining 7648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3073 17.99 - 35.98: 235 35.98 - 53.97: 45 53.97 - 71.96: 3 71.96 - 89.95: 4 Dihedral angle restraints: 3360 sinusoidal: 1302 harmonic: 2058 Sorted by residual: dihedral pdb=" N PHE A 649 " pdb=" C PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta harmonic sigma weight residual 122.80 139.31 -16.51 0 2.50e+00 1.60e-01 4.36e+01 dihedral pdb=" C PHE A 649 " pdb=" N PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta harmonic sigma weight residual -122.60 -139.03 16.43 0 2.50e+00 1.60e-01 4.32e+01 dihedral pdb=" CA PHE A 722 " pdb=" C PHE A 722 " pdb=" N LEU A 723 " pdb=" CA LEU A 723 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 3357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 905 0.135 - 0.270: 8 0.270 - 0.405: 0 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 914 Sorted by residual: chirality pdb=" CA PHE A 649 " pdb=" N PHE A 649 " pdb=" C PHE A 649 " pdb=" CB PHE A 649 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CB ILE A 137 " pdb=" CA ILE A 137 " pdb=" CG1 ILE A 137 " pdb=" CG2 ILE A 137 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 911 not shown) Planarity restraints: 967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 406 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO A 407 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 417 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 418 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 649 " 0.016 2.00e-02 2.50e+03 1.29e-02 2.91e+00 pdb=" CG PHE A 649 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 649 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 649 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 649 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 649 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 649 " 0.001 2.00e-02 2.50e+03 ... (remaining 964 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 936 2.76 - 3.30: 5906 3.30 - 3.83: 9048 3.83 - 4.37: 10106 4.37 - 4.90: 16840 Nonbonded interactions: 42836 Sorted by model distance: nonbonded pdb=" N ASP A 142 " pdb=" OE2 GLU A 146 " model vdw 2.226 2.520 nonbonded pdb=" O MET A 610 " pdb=" OH TYR A 622 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR A 61 " pdb=" O VAL A 513 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR A 680 " pdb=" NH2 ARG A 720 " model vdw 2.305 2.520 nonbonded pdb=" O GLY A 426 " pdb=" OH TYR A 431 " model vdw 2.306 2.440 ... (remaining 42831 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=1.00 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.250 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5624 Z= 0.265 Angle : 0.918 11.022 7653 Z= 0.501 Chirality : 0.052 0.675 914 Planarity : 0.006 0.075 967 Dihedral : 13.382 89.947 2036 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.17 % Allowed : 1.19 % Favored : 98.64 % Cbeta Deviations : 0.15 % 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: -1.30 (0.30), residues: 719 helix: -0.15 (0.24), residues: 457 sheet: -3.15 (0.69), residues: 31 loop : -1.78 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 737 HIS 0.005 0.001 HIS A 540 PHE 0.029 0.002 PHE A 649 TYR 0.025 0.002 TYR A 151 ARG 0.006 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.567 Fit side-chains REVERT: A 128 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7275 (tp-100) REVERT: A 147 ILE cc_start: 0.8233 (pt) cc_final: 0.7427 (pt) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1410 time to fit residues: 24.3852 Evaluate side-chains 117 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5624 Z= 0.261 Angle : 0.808 7.728 7653 Z= 0.407 Chirality : 0.046 0.195 914 Planarity : 0.006 0.070 967 Dihedral : 5.442 24.377 769 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.15 % Favored : 94.71 % Rotamer: Outliers : 2.72 % Allowed : 12.93 % Favored : 84.35 % 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: -1.30 (0.30), residues: 719 helix: -0.07 (0.23), residues: 459 sheet: -3.33 (0.69), residues: 31 loop : -1.99 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 737 HIS 0.006 0.002 HIS A 540 PHE 0.020 0.002 PHE A 649 TYR 0.017 0.002 TYR A 151 ARG 0.006 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.575 Fit side-chains REVERT: A 44 TYR cc_start: 0.7309 (m-10) cc_final: 0.6857 (m-10) REVERT: A 128 GLN cc_start: 0.7883 (tp-100) cc_final: 0.7401 (tp-100) REVERT: A 419 LEU cc_start: 0.6416 (pp) cc_final: 0.6207 (pp) REVERT: A 620 MET cc_start: 0.6584 (tpp) cc_final: 0.6197 (ptm) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.1374 time to fit residues: 23.2843 Evaluate side-chains 125 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5624 Z= 0.283 Angle : 0.819 7.745 7653 Z= 0.417 Chirality : 0.047 0.305 914 Planarity : 0.006 0.056 967 Dihedral : 5.583 24.273 767 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 5.27 % Allowed : 15.14 % Favored : 79.59 % 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: -1.28 (0.30), residues: 719 helix: -0.06 (0.24), residues: 453 sheet: -3.35 (0.67), residues: 36 loop : -1.85 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 737 HIS 0.007 0.002 HIS A 540 PHE 0.021 0.002 PHE A 649 TYR 0.017 0.002 TYR A 151 ARG 0.007 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7474 (m-10) cc_final: 0.6832 (m-10) REVERT: A 116 ASP cc_start: 0.6637 (OUTLIER) cc_final: 0.6435 (m-30) REVERT: A 128 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7388 (tp-100) REVERT: A 480 LYS cc_start: 0.6287 (mmtm) cc_final: 0.5433 (mmtm) REVERT: A 620 MET cc_start: 0.6679 (tpp) cc_final: 0.6366 (tpp) REVERT: A 742 MET cc_start: -0.2255 (tpt) cc_final: -0.3483 (tpt) outliers start: 31 outliers final: 23 residues processed: 135 average time/residue: 0.1643 time to fit residues: 28.9872 Evaluate side-chains 139 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 717 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5624 Z= 0.213 Angle : 0.744 6.984 7653 Z= 0.372 Chirality : 0.044 0.220 914 Planarity : 0.005 0.046 967 Dihedral : 5.318 22.029 767 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 6.46 % Allowed : 16.16 % Favored : 77.38 % 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: -1.18 (0.31), residues: 719 helix: 0.07 (0.24), residues: 462 sheet: -3.17 (0.67), residues: 44 loop : -1.97 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.004 0.001 HIS A 540 PHE 0.022 0.002 PHE A 449 TYR 0.019 0.002 TYR A 151 ARG 0.004 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7470 (m-10) cc_final: 0.6826 (m-10) REVERT: A 65 ARG cc_start: 0.6794 (mpt-90) cc_final: 0.6484 (mpt-90) REVERT: A 128 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7330 (tp-100) REVERT: A 470 THR cc_start: 0.5572 (OUTLIER) cc_final: 0.4676 (p) REVERT: A 480 LYS cc_start: 0.6110 (mmtm) cc_final: 0.5278 (mttm) REVERT: A 620 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6191 (ptm) REVERT: A 631 MET cc_start: 0.7094 (tpt) cc_final: 0.6688 (mmm) REVERT: A 674 THR cc_start: 0.5078 (OUTLIER) cc_final: 0.3305 (t) REVERT: A 742 MET cc_start: -0.2267 (tpt) cc_final: -0.3463 (tpt) outliers start: 38 outliers final: 23 residues processed: 142 average time/residue: 0.1548 time to fit residues: 29.0687 Evaluate side-chains 142 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 708 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 17 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5535 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5624 Z= 0.189 Angle : 0.719 8.917 7653 Z= 0.350 Chirality : 0.044 0.353 914 Planarity : 0.005 0.039 967 Dihedral : 5.000 21.045 767 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer: Outliers : 5.27 % Allowed : 18.71 % Favored : 76.02 % 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: -0.74 (0.31), residues: 719 helix: 0.43 (0.24), residues: 464 sheet: -2.98 (0.68), residues: 44 loop : -1.87 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.003 0.001 HIS A 37 PHE 0.018 0.001 PHE A 265 TYR 0.018 0.001 TYR A 151 ARG 0.010 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7365 (m-10) cc_final: 0.6836 (m-10) REVERT: A 65 ARG cc_start: 0.6778 (mpt-90) cc_final: 0.6468 (mpt-90) REVERT: A 128 GLN cc_start: 0.7765 (tp-100) cc_final: 0.7455 (tp-100) REVERT: A 253 ILE cc_start: 0.7254 (mm) cc_final: 0.7021 (mm) REVERT: A 273 TYR cc_start: 0.6123 (m-10) cc_final: 0.4825 (m-10) REVERT: A 480 LYS cc_start: 0.5929 (mmtm) cc_final: 0.5095 (mttm) REVERT: A 534 ARG cc_start: 0.6878 (mmt-90) cc_final: 0.6623 (mmt-90) REVERT: A 631 MET cc_start: 0.6988 (tpt) cc_final: 0.6667 (mmm) REVERT: A 742 MET cc_start: -0.2255 (tpt) cc_final: -0.3350 (tpt) outliers start: 31 outliers final: 25 residues processed: 133 average time/residue: 0.1600 time to fit residues: 27.9284 Evaluate side-chains 142 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 717 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 20.0000 chunk 62 optimal weight: 0.0010 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5624 Z= 0.206 Angle : 0.729 8.514 7653 Z= 0.356 Chirality : 0.043 0.251 914 Planarity : 0.005 0.041 967 Dihedral : 4.979 20.878 767 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.70 % Favored : 94.16 % Rotamer: Outliers : 5.61 % Allowed : 19.73 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.31), residues: 719 helix: 0.41 (0.24), residues: 468 sheet: -3.12 (0.68), residues: 44 loop : -1.94 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 640 HIS 0.003 0.001 HIS A 540 PHE 0.018 0.002 PHE A 649 TYR 0.019 0.002 TYR A 151 ARG 0.004 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7532 (m-10) cc_final: 0.6909 (m-10) REVERT: A 128 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7507 (tp-100) REVERT: A 271 GLU cc_start: 0.5251 (mt-10) cc_final: 0.4806 (mt-10) REVERT: A 273 TYR cc_start: 0.6316 (m-10) cc_final: 0.5079 (m-10) REVERT: A 419 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5671 (pp) REVERT: A 470 THR cc_start: 0.5841 (OUTLIER) cc_final: 0.5081 (p) REVERT: A 480 LYS cc_start: 0.6116 (mmtm) cc_final: 0.5183 (mttm) REVERT: A 534 ARG cc_start: 0.6949 (mmt-90) cc_final: 0.6680 (mmt90) REVERT: A 631 MET cc_start: 0.7042 (tpt) cc_final: 0.6673 (mmm) REVERT: A 662 MET cc_start: 0.5397 (mmm) cc_final: 0.5030 (mmm) REVERT: A 742 MET cc_start: -0.2273 (tpt) cc_final: -0.3328 (tpt) outliers start: 33 outliers final: 27 residues processed: 136 average time/residue: 0.1735 time to fit residues: 30.8245 Evaluate side-chains 145 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 717 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5624 Z= 0.196 Angle : 0.741 12.037 7653 Z= 0.356 Chirality : 0.044 0.367 914 Planarity : 0.005 0.042 967 Dihedral : 4.934 20.699 767 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.29 % Favored : 94.58 % Rotamer: Outliers : 5.78 % Allowed : 19.22 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.32), residues: 719 helix: 0.50 (0.25), residues: 466 sheet: -3.11 (0.68), residues: 44 loop : -1.96 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 640 HIS 0.002 0.001 HIS A 540 PHE 0.017 0.001 PHE A 265 TYR 0.019 0.001 TYR A 151 ARG 0.004 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7515 (m-10) cc_final: 0.6946 (m-10) REVERT: A 213 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7115 (mp) REVERT: A 273 TYR cc_start: 0.6191 (m-10) cc_final: 0.4970 (m-10) REVERT: A 419 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.6019 (pp) REVERT: A 470 THR cc_start: 0.5739 (OUTLIER) cc_final: 0.5002 (p) REVERT: A 480 LYS cc_start: 0.6330 (mmtm) cc_final: 0.5358 (mttm) REVERT: A 534 ARG cc_start: 0.6960 (mmt-90) cc_final: 0.6630 (mmt90) REVERT: A 631 MET cc_start: 0.7049 (tpt) cc_final: 0.6686 (mmm) REVERT: A 642 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7307 (tt) REVERT: A 662 MET cc_start: 0.5343 (mmm) cc_final: 0.5008 (mmm) REVERT: A 742 MET cc_start: -0.2487 (tpt) cc_final: -0.3474 (tpt) outliers start: 34 outliers final: 27 residues processed: 134 average time/residue: 0.1646 time to fit residues: 28.8581 Evaluate side-chains 146 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 717 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5624 Z= 0.325 Angle : 0.845 11.419 7653 Z= 0.425 Chirality : 0.047 0.344 914 Planarity : 0.006 0.043 967 Dihedral : 5.522 24.525 767 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.51 % Favored : 92.35 % Rotamer: Outliers : 6.63 % Allowed : 19.22 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.31), residues: 719 helix: 0.12 (0.24), residues: 463 sheet: -3.33 (0.68), residues: 36 loop : -2.02 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 737 HIS 0.006 0.002 HIS A 540 PHE 0.025 0.003 PHE A 389 TYR 0.019 0.002 TYR A 151 ARG 0.007 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7641 (m-10) cc_final: 0.6941 (m-10) REVERT: A 128 GLN cc_start: 0.7801 (tp40) cc_final: 0.7462 (tp-100) REVERT: A 271 GLU cc_start: 0.5497 (mt-10) cc_final: 0.4774 (mt-10) REVERT: A 273 TYR cc_start: 0.6285 (m-10) cc_final: 0.5116 (m-10) REVERT: A 419 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6136 (pp) REVERT: A 470 THR cc_start: 0.5900 (OUTLIER) cc_final: 0.5237 (p) REVERT: A 480 LYS cc_start: 0.6641 (mmtm) cc_final: 0.5777 (mttm) REVERT: A 631 MET cc_start: 0.7368 (tpt) cc_final: 0.6871 (mmm) REVERT: A 642 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7169 (tt) REVERT: A 674 THR cc_start: 0.5106 (OUTLIER) cc_final: 0.3424 (t) REVERT: A 742 MET cc_start: -0.2386 (tpt) cc_final: -0.3407 (tpt) outliers start: 39 outliers final: 29 residues processed: 137 average time/residue: 0.1615 time to fit residues: 28.9891 Evaluate side-chains 145 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 717 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5624 Z= 0.219 Angle : 0.789 10.679 7653 Z= 0.381 Chirality : 0.044 0.287 914 Planarity : 0.005 0.041 967 Dihedral : 5.280 24.075 767 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.29 % Favored : 94.58 % Rotamer: Outliers : 5.61 % Allowed : 20.92 % Favored : 73.47 % 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: -0.96 (0.31), residues: 719 helix: 0.32 (0.24), residues: 459 sheet: -3.45 (0.65), residues: 44 loop : -1.94 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 86 HIS 0.004 0.001 HIS A 540 PHE 0.021 0.002 PHE A 265 TYR 0.019 0.002 TYR A 151 ARG 0.004 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7583 (m-10) cc_final: 0.6893 (m-10) REVERT: A 271 GLU cc_start: 0.5403 (mt-10) cc_final: 0.4757 (mt-10) REVERT: A 273 TYR cc_start: 0.6267 (m-10) cc_final: 0.4969 (m-10) REVERT: A 419 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.6010 (pp) REVERT: A 480 LYS cc_start: 0.6323 (mmtm) cc_final: 0.5338 (mttm) REVERT: A 499 LYS cc_start: 0.7196 (mmmt) cc_final: 0.6873 (mmmt) REVERT: A 631 MET cc_start: 0.7246 (tpt) cc_final: 0.6813 (mmm) REVERT: A 642 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7246 (tt) REVERT: A 662 MET cc_start: 0.5423 (mmm) cc_final: 0.5049 (mmm) REVERT: A 742 MET cc_start: -0.2376 (tpt) cc_final: -0.3399 (tpt) outliers start: 33 outliers final: 27 residues processed: 130 average time/residue: 0.1742 time to fit residues: 29.5073 Evaluate side-chains 138 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 708 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 66 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5624 Z= 0.268 Angle : 0.832 11.229 7653 Z= 0.409 Chirality : 0.046 0.404 914 Planarity : 0.006 0.042 967 Dihedral : 5.446 25.693 767 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.23 % Favored : 92.63 % Rotamer: Outliers : 5.44 % Allowed : 21.77 % Favored : 72.79 % 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: -1.04 (0.31), residues: 719 helix: 0.22 (0.24), residues: 458 sheet: -3.37 (0.69), residues: 36 loop : -2.00 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 86 HIS 0.006 0.001 HIS A 540 PHE 0.021 0.002 PHE A 389 TYR 0.022 0.002 TYR A 151 ARG 0.012 0.001 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.7683 (m-10) cc_final: 0.6914 (m-10) REVERT: A 65 ARG cc_start: 0.6721 (mpt-90) cc_final: 0.6415 (mpt-90) REVERT: A 125 MET cc_start: 0.6906 (ttt) cc_final: 0.6408 (ttt) REVERT: A 271 GLU cc_start: 0.5478 (mt-10) cc_final: 0.4794 (mt-10) REVERT: A 273 TYR cc_start: 0.6335 (m-10) cc_final: 0.5052 (m-10) REVERT: A 419 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6103 (pp) REVERT: A 480 LYS cc_start: 0.6371 (mmtm) cc_final: 0.5433 (mttm) REVERT: A 642 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7126 (tt) REVERT: A 662 MET cc_start: 0.5467 (mmm) cc_final: 0.5072 (mmm) REVERT: A 742 MET cc_start: -0.2357 (tpt) cc_final: -0.3384 (tpt) outliers start: 32 outliers final: 29 residues processed: 131 average time/residue: 0.1855 time to fit residues: 31.6658 Evaluate side-chains 143 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 708 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.261253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.244449 restraints weight = 9189.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.249825 restraints weight = 8186.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.251843 restraints weight = 3803.389| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5624 Z= 0.229 Angle : 0.793 11.373 7653 Z= 0.386 Chirality : 0.045 0.347 914 Planarity : 0.005 0.051 967 Dihedral : 5.334 25.294 767 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.70 % Favored : 94.16 % Rotamer: Outliers : 4.93 % Allowed : 21.94 % Favored : 73.13 % 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: -0.95 (0.31), residues: 719 helix: 0.35 (0.24), residues: 457 sheet: -3.47 (0.66), residues: 44 loop : -2.00 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.004 0.001 HIS A 540 PHE 0.020 0.002 PHE A 265 TYR 0.022 0.002 TYR A 151 ARG 0.011 0.001 ARG A 63 =============================================================================== Job complete usr+sys time: 1211.26 seconds wall clock time: 22 minutes 28.42 seconds (1348.42 seconds total)