Starting phenix.real_space_refine on Wed Feb 12 12:38:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a69_6987/02_2025/6a69_6987.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a69_6987/02_2025/6a69_6987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6a69_6987/02_2025/6a69_6987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a69_6987/02_2025/6a69_6987.map" model { file = "/net/cci-nas-00/data/ceres_data/6a69_6987/02_2025/6a69_6987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a69_6987/02_2025/6a69_6987.cif" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 39 5.16 5 C 5045 2.51 5 N 1324 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7851 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 6839 Classifications: {'peptide': 911} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 36, 'TRANS': 847} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 998 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1014 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.11, per 1000 atoms: 0.65 Number of scatterers: 7851 At special positions: 0 Unit cell: (134.193, 103.645, 128.738, 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 39 16.00 O 1443 8.00 N 1324 7.00 C 5045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 200 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 301 " - " ASN B 168 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 9 sheets defined 43.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 153 through 190 removed outlier: 3.994A pdb=" N ALA A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 362 through 397 removed outlier: 3.815A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.969A pdb=" N VAL A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.945A pdb=" N MET A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.733A pdb=" N CYS A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 removed outlier: 4.086A pdb=" N VAL A 563 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 625 through 632 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.842A pdb=" N LYS A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.973A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.857A pdb=" N LEU A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 834 through 877 removed outlier: 3.726A pdb=" N ILE A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 Processing helix chain 'A' and resid 896 through 903 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.672A pdb=" N LEU A 912 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 913 " --> pdb=" O SER A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 925 through 949 Processing helix chain 'A' and resid 970 through 990 removed outlier: 3.667A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1026 removed outlier: 4.004A pdb=" N LEU A1014 " --> pdb=" O CYS A1010 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A1025 " --> pdb=" O ILE A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1058 removed outlier: 3.913A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 245 removed outlier: 3.533A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.982A pdb=" N ILE A 472 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 707 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER A 474 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEU A 765 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N MET A 706 " --> pdb=" O LEU A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.866A pdb=" N GLU A 683 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 589 removed outlier: 3.650A pdb=" N MET A 585 " --> pdb=" O LYS A 601 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 613 through 616 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 126 removed outlier: 6.471A pdb=" N LYS B 144 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 143 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 6.202A pdb=" N GLU B 131 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 211 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 200 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 197 " --> pdb=" O LYS B 158 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1038 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: 2.40 Time building geometry restraints manager: 2.18 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: 2391 1.34 - 1.46: 1487 1.46 - 1.58: 4055 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 7994 Sorted by residual: bond pdb=" C TRP A 759 " pdb=" N PRO A 760 " ideal model delta sigma weight residual 1.331 1.364 -0.032 7.90e-03 1.60e+04 1.64e+01 bond pdb=" C ALA B 222 " pdb=" N PRO B 223 " ideal model delta sigma weight residual 1.333 1.363 -0.030 7.80e-03 1.64e+04 1.46e+01 bond pdb=" CG GLN A1020 " pdb=" CD GLN A1020 " ideal model delta sigma weight residual 1.516 1.452 0.064 2.50e-02 1.60e+03 6.61e+00 bond pdb=" CB TRP A 759 " pdb=" CG TRP A 759 " ideal model delta sigma weight residual 1.498 1.423 0.075 3.10e-02 1.04e+03 5.81e+00 bond pdb=" CB VAL A 792 " pdb=" CG2 VAL A 792 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.40e+00 ... (remaining 7989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 10327 2.96 - 5.91: 425 5.91 - 8.87: 86 8.87 - 11.82: 22 11.82 - 14.78: 6 Bond angle restraints: 10866 Sorted by residual: angle pdb=" C HIS A 965 " pdb=" N ALA A 966 " pdb=" CA ALA A 966 " ideal model delta sigma weight residual 121.70 134.77 -13.07 1.80e+00 3.09e-01 5.28e+01 angle pdb=" N HIS A 965 " pdb=" CA HIS A 965 " pdb=" C HIS A 965 " ideal model delta sigma weight residual 111.07 118.76 -7.69 1.07e+00 8.73e-01 5.17e+01 angle pdb=" C SER A 642 " pdb=" N GLU A 643 " pdb=" CA GLU A 643 " ideal model delta sigma weight residual 121.70 134.07 -12.37 1.80e+00 3.09e-01 4.72e+01 angle pdb=" N GLY A 228 " pdb=" CA GLY A 228 " pdb=" C GLY A 228 " ideal model delta sigma weight residual 111.42 121.78 -10.36 1.51e+00 4.39e-01 4.71e+01 angle pdb=" N PRO A 67 " pdb=" CA PRO A 67 " pdb=" CB PRO A 67 " ideal model delta sigma weight residual 103.00 110.36 -7.36 1.10e+00 8.26e-01 4.48e+01 ... (remaining 10861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 4389 15.21 - 30.42: 325 30.42 - 45.64: 74 45.64 - 60.85: 11 60.85 - 76.06: 4 Dihedral angle restraints: 4803 sinusoidal: 1822 harmonic: 2981 Sorted by residual: dihedral pdb=" CA VAL A 680 " pdb=" C VAL A 680 " pdb=" N GLY A 681 " pdb=" CA GLY A 681 " ideal model delta harmonic sigma weight residual 180.00 126.37 53.63 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA ASN A 565 " pdb=" C ASN A 565 " pdb=" N GLU A 566 " pdb=" CA GLU A 566 " ideal model delta harmonic sigma weight residual 0.00 44.37 -44.37 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA PHE A 953 " pdb=" C PHE A 953 " pdb=" N PHE A 954 " pdb=" CA PHE A 954 " ideal model delta harmonic sigma weight residual -180.00 -137.23 -42.77 0 5.00e+00 4.00e-02 7.32e+01 ... (remaining 4800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1015 0.080 - 0.160: 260 0.160 - 0.240: 28 0.240 - 0.320: 4 0.320 - 0.400: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CB ILE A1061 " pdb=" CA ILE A1061 " pdb=" CG1 ILE A1061 " pdb=" CG2 ILE A1061 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA HIS A 965 " pdb=" N HIS A 965 " pdb=" C HIS A 965 " pdb=" CB HIS A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL A 680 " pdb=" CA VAL A 680 " pdb=" CG1 VAL A 680 " pdb=" CG2 VAL A 680 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1305 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 94 " -0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO A 95 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 638 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 639 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 225 " 0.015 2.00e-02 2.50e+03 1.81e-02 8.22e+00 pdb=" CG TRP B 225 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 225 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 225 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 225 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 225 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 225 " 0.001 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2026 2.80 - 3.32: 7367 3.32 - 3.85: 12435 3.85 - 4.37: 13360 4.37 - 4.90: 22735 Nonbonded interactions: 57923 Sorted by model distance: nonbonded pdb=" O VAL A 515 " pdb=" OG SER A 519 " model vdw 2.275 3.040 nonbonded pdb=" O TYR A 513 " pdb=" OG1 THR A 516 " model vdw 2.308 3.040 nonbonded pdb=" O LEU A 947 " pdb=" NH1 ARG A 960 " model vdw 2.344 3.120 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 125 " model vdw 2.345 3.040 nonbonded pdb=" OE2 GLU B 135 " pdb=" NE2 GLN B 190 " model vdw 2.350 3.120 ... (remaining 57918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.250 Find NCS groups from input model: 0.090 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.011 0.105 7994 Z= 0.689 Angle : 1.480 14.780 10866 Z= 0.816 Chirality : 0.069 0.400 1308 Planarity : 0.009 0.077 1372 Dihedral : 11.870 76.061 2872 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.53 % Favored : 86.37 % Rotamer: Outliers : 1.81 % Allowed : 4.58 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.43 % Twisted Proline : 0.00 % Twisted General : 0.91 % 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: -4.69 (0.21), residues: 1021 helix: -2.43 (0.19), residues: 449 sheet: -2.74 (0.46), residues: 103 loop : -3.93 (0.22), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP B 225 HIS 0.009 0.003 HIS A 265 PHE 0.036 0.004 PHE A 953 TYR 0.032 0.003 TYR A 445 ARG 0.008 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8688 (mt-10) REVERT: A 217 GLN cc_start: 0.8337 (tt0) cc_final: 0.7862 (tp40) REVERT: A 235 ASP cc_start: 0.8010 (m-30) cc_final: 0.7804 (t0) REVERT: A 466 MET cc_start: 0.8832 (tmm) cc_final: 0.8292 (tmm) REVERT: A 752 GLN cc_start: 0.8888 (tt0) cc_final: 0.8684 (tm-30) REVERT: A 814 MET cc_start: 0.8765 (mmp) cc_final: 0.8411 (mmp) REVERT: A 859 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8992 (tm-30) REVERT: A 887 MET cc_start: 0.8963 (tpp) cc_final: 0.8445 (tpp) REVERT: A 911 LEU cc_start: 0.9705 (mt) cc_final: 0.9472 (mp) REVERT: A 1017 PHE cc_start: 0.8919 (t80) cc_final: 0.8647 (t80) REVERT: B 218 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7903 (mtp-110) outliers start: 15 outliers final: 6 residues processed: 240 average time/residue: 0.1943 time to fit residues: 64.4276 Evaluate side-chains 145 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 540 HIS A 711 ASN A 886 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 HIS ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.140061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106411 restraints weight = 21761.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105514 restraints weight = 12630.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105816 restraints weight = 12400.024| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7994 Z= 0.210 Angle : 0.810 12.817 10866 Z= 0.421 Chirality : 0.047 0.198 1308 Planarity : 0.007 0.072 1372 Dihedral : 6.953 40.364 1111 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.33 % Favored : 91.47 % Rotamer: Outliers : 0.24 % Allowed : 3.74 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.11 (0.24), residues: 1021 helix: -0.55 (0.23), residues: 462 sheet: -2.80 (0.42), residues: 113 loop : -3.60 (0.24), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 225 HIS 0.007 0.001 HIS A 971 PHE 0.025 0.002 PHE A 953 TYR 0.013 0.001 TYR B 244 ARG 0.009 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8159 (mp0) REVERT: A 217 GLN cc_start: 0.8242 (tt0) cc_final: 0.7975 (tp40) REVERT: A 235 ASP cc_start: 0.7999 (m-30) cc_final: 0.7794 (t0) REVERT: A 268 GLU cc_start: 0.8224 (pp20) cc_final: 0.7925 (pp20) REVERT: A 411 ILE cc_start: 0.9262 (tp) cc_final: 0.8967 (mm) REVERT: A 421 ILE cc_start: 0.9598 (tp) cc_final: 0.9378 (tp) REVERT: A 466 MET cc_start: 0.8664 (tmm) cc_final: 0.7978 (tmm) REVERT: A 887 MET cc_start: 0.8891 (tpp) cc_final: 0.8525 (tpp) REVERT: A 1006 ASN cc_start: 0.8475 (m-40) cc_final: 0.7709 (m-40) REVERT: B 157 LYS cc_start: 0.6269 (tptp) cc_final: 0.5640 (mmmt) REVERT: B 199 GLU cc_start: 0.5428 (pt0) cc_final: 0.5205 (pt0) outliers start: 2 outliers final: 2 residues processed: 219 average time/residue: 0.1640 time to fit residues: 51.5152 Evaluate side-chains 137 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106385 restraints weight = 16275.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107030 restraints weight = 10145.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107749 restraints weight = 7718.906| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7994 Z= 0.193 Angle : 0.773 12.646 10866 Z= 0.400 Chirality : 0.046 0.191 1308 Planarity : 0.006 0.085 1372 Dihedral : 6.455 40.082 1111 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.61 % Favored : 90.20 % Rotamer: Outliers : 0.12 % Allowed : 1.93 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.44 (0.25), residues: 1021 helix: 0.18 (0.24), residues: 461 sheet: -2.55 (0.44), residues: 113 loop : -3.42 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 225 HIS 0.005 0.001 HIS A 971 PHE 0.019 0.001 PHE A 953 TYR 0.011 0.001 TYR A 445 ARG 0.004 0.000 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8083 (mp0) REVERT: A 268 GLU cc_start: 0.8275 (pp20) cc_final: 0.7901 (pp20) REVERT: A 466 MET cc_start: 0.8731 (tmm) cc_final: 0.8076 (tmm) REVERT: A 482 MET cc_start: 0.7794 (mmm) cc_final: 0.7511 (mmm) REVERT: A 887 MET cc_start: 0.8949 (tpp) cc_final: 0.8481 (tpp) REVERT: A 928 MET cc_start: 0.8343 (tpp) cc_final: 0.7923 (tpp) REVERT: A 1006 ASN cc_start: 0.8362 (m-40) cc_final: 0.7833 (m-40) REVERT: B 131 GLU cc_start: 0.6407 (tp30) cc_final: 0.6185 (tp30) REVERT: B 157 LYS cc_start: 0.6339 (tptp) cc_final: 0.6044 (tptt) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1622 time to fit residues: 43.0915 Evaluate side-chains 131 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.142148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107479 restraints weight = 19872.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107311 restraints weight = 11571.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107835 restraints weight = 10381.052| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 7994 Z= 0.206 Angle : 0.723 12.339 10866 Z= 0.378 Chirality : 0.045 0.188 1308 Planarity : 0.006 0.085 1372 Dihedral : 6.014 40.854 1111 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.82 % Favored : 90.98 % Rotamer: Outliers : 0.24 % Allowed : 3.38 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.11 (0.26), residues: 1021 helix: 0.56 (0.25), residues: 457 sheet: -2.39 (0.44), residues: 113 loop : -3.35 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 759 HIS 0.004 0.001 HIS A 971 PHE 0.016 0.001 PHE A 954 TYR 0.009 0.001 TYR A 938 ARG 0.004 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLN cc_start: 0.7736 (tp40) cc_final: 0.7284 (mm110) REVERT: A 267 MET cc_start: 0.8471 (mmm) cc_final: 0.8199 (mmp) REVERT: A 268 GLU cc_start: 0.8030 (pp20) cc_final: 0.7818 (pp20) REVERT: A 466 MET cc_start: 0.8743 (tmm) cc_final: 0.8122 (tmm) REVERT: A 482 MET cc_start: 0.7876 (mmm) cc_final: 0.7519 (mmm) REVERT: A 887 MET cc_start: 0.8986 (tpp) cc_final: 0.8773 (tpp) REVERT: A 905 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 157 LYS cc_start: 0.6489 (tptp) cc_final: 0.5984 (mmmt) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.1545 time to fit residues: 41.4679 Evaluate side-chains 131 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 40.0000 chunk 40 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106743 restraints weight = 19233.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106846 restraints weight = 10938.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107019 restraints weight = 10561.414| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7994 Z= 0.211 Angle : 0.721 12.043 10866 Z= 0.378 Chirality : 0.045 0.178 1308 Planarity : 0.006 0.091 1372 Dihedral : 5.860 40.819 1111 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.82 % Favored : 90.98 % Rotamer: Outliers : 0.12 % Allowed : 1.93 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.95 (0.26), residues: 1021 helix: 0.62 (0.25), residues: 457 sheet: -2.02 (0.46), residues: 106 loop : -3.26 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 PHE 0.016 0.001 PHE A 954 TYR 0.018 0.001 TYR A 560 ARG 0.005 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8093 (mp0) REVERT: A 267 MET cc_start: 0.8468 (mmm) cc_final: 0.8205 (mmp) REVERT: A 268 GLU cc_start: 0.8025 (pp20) cc_final: 0.7771 (pp20) REVERT: A 466 MET cc_start: 0.8762 (tmm) cc_final: 0.8380 (tmm) REVERT: A 482 MET cc_start: 0.7858 (mmm) cc_final: 0.7491 (mmm) REVERT: A 485 MET cc_start: 0.7831 (pmm) cc_final: 0.7551 (pmm) REVERT: A 757 LYS cc_start: 0.8470 (mmpt) cc_final: 0.8096 (mmtp) REVERT: A 905 GLU cc_start: 0.8210 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 928 MET cc_start: 0.8358 (tpp) cc_final: 0.7912 (tpp) REVERT: A 998 ASN cc_start: 0.8223 (t0) cc_final: 0.7808 (t0) REVERT: B 157 LYS cc_start: 0.6573 (tptp) cc_final: 0.5977 (mmmt) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1555 time to fit residues: 42.2742 Evaluate side-chains 133 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 62 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107702 restraints weight = 27708.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109160 restraints weight = 18709.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112196 restraints weight = 11399.852| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7994 Z= 0.199 Angle : 0.703 12.098 10866 Z= 0.367 Chirality : 0.044 0.181 1308 Planarity : 0.006 0.091 1372 Dihedral : 5.718 41.364 1111 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.94 % Favored : 91.86 % Rotamer: Outliers : 0.12 % Allowed : 1.69 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.72 (0.26), residues: 1021 helix: 0.83 (0.25), residues: 454 sheet: -1.89 (0.47), residues: 106 loop : -3.14 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 PHE 0.012 0.001 PHE A 954 TYR 0.009 0.001 TYR A 497 ARG 0.002 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8063 (mp0) REVERT: A 267 MET cc_start: 0.8480 (mmm) cc_final: 0.8256 (mmp) REVERT: A 268 GLU cc_start: 0.8087 (pp20) cc_final: 0.7867 (pp20) REVERT: A 451 MET cc_start: 0.8235 (tpp) cc_final: 0.8027 (tmm) REVERT: A 466 MET cc_start: 0.8796 (tmm) cc_final: 0.8448 (tmm) REVERT: A 482 MET cc_start: 0.7806 (mmm) cc_final: 0.7470 (mmm) REVERT: A 757 LYS cc_start: 0.8332 (mmpt) cc_final: 0.7899 (mptt) REVERT: A 887 MET cc_start: 0.8721 (tpp) cc_final: 0.8290 (tpp) REVERT: A 998 ASN cc_start: 0.8158 (t0) cc_final: 0.7922 (t0) REVERT: A 1020 GLN cc_start: 0.8666 (tp40) cc_final: 0.8364 (tp40) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1598 time to fit residues: 41.5805 Evaluate side-chains 131 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN A 857 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108895 restraints weight = 27693.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110800 restraints weight = 17865.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110638 restraints weight = 15038.074| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7994 Z= 0.187 Angle : 0.693 11.997 10866 Z= 0.362 Chirality : 0.044 0.188 1308 Planarity : 0.006 0.097 1372 Dihedral : 5.629 40.823 1111 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.92 % Favored : 90.98 % Rotamer: Outliers : 0.12 % Allowed : 1.09 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.52 (0.26), residues: 1021 helix: 0.98 (0.25), residues: 454 sheet: -1.70 (0.48), residues: 110 loop : -3.04 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 PHE 0.031 0.001 PHE A 953 TYR 0.007 0.001 TYR A 445 ARG 0.002 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8054 (mp0) REVERT: A 267 MET cc_start: 0.8510 (mmm) cc_final: 0.8261 (mmp) REVERT: A 268 GLU cc_start: 0.8095 (pp20) cc_final: 0.7822 (pp20) REVERT: A 466 MET cc_start: 0.8750 (tmm) cc_final: 0.8450 (tmm) REVERT: A 482 MET cc_start: 0.7631 (mmm) cc_final: 0.7355 (mmm) REVERT: A 485 MET cc_start: 0.7682 (pmm) cc_final: 0.7369 (pmm) REVERT: A 757 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7781 (mptt) REVERT: A 905 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 928 MET cc_start: 0.8200 (tpp) cc_final: 0.7809 (tpp) REVERT: A 998 ASN cc_start: 0.8273 (t0) cc_final: 0.7981 (t0) REVERT: B 141 MET cc_start: 0.6534 (mpp) cc_final: 0.6197 (mpp) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1601 time to fit residues: 41.4553 Evaluate side-chains 127 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 0.0370 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.0464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN A 711 ASN ** A 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104702 restraints weight = 30489.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105397 restraints weight = 19489.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105842 restraints weight = 16619.124| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7994 Z= 0.262 Angle : 0.727 11.684 10866 Z= 0.380 Chirality : 0.045 0.173 1308 Planarity : 0.006 0.099 1372 Dihedral : 5.626 42.746 1111 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.51 % Favored : 90.29 % Rotamer: Outliers : 0.12 % Allowed : 1.21 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.54 (0.26), residues: 1021 helix: 0.87 (0.25), residues: 458 sheet: -1.58 (0.49), residues: 110 loop : -3.01 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.005 0.001 HIS A 971 PHE 0.015 0.001 PHE A 953 TYR 0.011 0.001 TYR A 445 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8080 (mp0) REVERT: A 194 PHE cc_start: 0.8903 (t80) cc_final: 0.8668 (t80) REVERT: A 268 GLU cc_start: 0.8114 (pp20) cc_final: 0.7828 (pp20) REVERT: A 466 MET cc_start: 0.8764 (tmm) cc_final: 0.8490 (tmm) REVERT: A 482 MET cc_start: 0.7648 (mmm) cc_final: 0.7357 (mmm) REVERT: A 485 MET cc_start: 0.7740 (pmm) cc_final: 0.7472 (pmm) REVERT: A 757 LYS cc_start: 0.8322 (mmpt) cc_final: 0.7794 (mptt) REVERT: A 887 MET cc_start: 0.8648 (tpp) cc_final: 0.8422 (tpp) REVERT: A 928 MET cc_start: 0.8217 (tpp) cc_final: 0.7870 (tpp) REVERT: B 131 GLU cc_start: 0.6829 (tp30) cc_final: 0.6263 (tp30) outliers start: 1 outliers final: 1 residues processed: 169 average time/residue: 0.1618 time to fit residues: 39.5479 Evaluate side-chains 126 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 88 optimal weight: 0.5980 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107829 restraints weight = 19864.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108363 restraints weight = 10782.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108559 restraints weight = 9660.112| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7994 Z= 0.199 Angle : 0.709 11.793 10866 Z= 0.369 Chirality : 0.045 0.176 1308 Planarity : 0.006 0.101 1372 Dihedral : 5.548 42.525 1111 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.31 % Favored : 90.49 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.45 (0.26), residues: 1021 helix: 0.91 (0.25), residues: 461 sheet: -1.50 (0.49), residues: 110 loop : -2.96 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 PHE 0.017 0.001 PHE A 953 TYR 0.007 0.001 TYR A 445 ARG 0.004 0.000 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7973 (mp0) REVERT: A 194 PHE cc_start: 0.8884 (t80) cc_final: 0.8646 (t80) REVERT: A 268 GLU cc_start: 0.8003 (pp20) cc_final: 0.7665 (pp20) REVERT: A 380 MET cc_start: 0.8119 (tpp) cc_final: 0.7564 (tmm) REVERT: A 466 MET cc_start: 0.8773 (tmm) cc_final: 0.8534 (tmm) REVERT: A 482 MET cc_start: 0.7601 (mmm) cc_final: 0.7304 (mmm) REVERT: A 485 MET cc_start: 0.7701 (pmm) cc_final: 0.7429 (pmm) REVERT: A 757 LYS cc_start: 0.8247 (mmpt) cc_final: 0.7722 (mptt) REVERT: A 887 MET cc_start: 0.8710 (tpp) cc_final: 0.8480 (tpp) REVERT: A 928 MET cc_start: 0.8225 (tpp) cc_final: 0.7962 (tpp) REVERT: B 131 GLU cc_start: 0.6637 (tp30) cc_final: 0.6060 (tp30) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1628 time to fit residues: 37.6734 Evaluate side-chains 123 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 711 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106456 restraints weight = 27584.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107175 restraints weight = 15962.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107556 restraints weight = 13076.271| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7994 Z= 0.230 Angle : 0.718 11.626 10866 Z= 0.373 Chirality : 0.045 0.177 1308 Planarity : 0.006 0.099 1372 Dihedral : 5.584 42.617 1111 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.22 % Favored : 90.59 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.39 (0.26), residues: 1021 helix: 0.95 (0.25), residues: 462 sheet: -1.39 (0.50), residues: 110 loop : -2.95 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 PHE 0.017 0.001 PHE A 953 TYR 0.009 0.001 TYR A 445 ARG 0.003 0.000 ARG A 705 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7991 (mp0) REVERT: A 192 GLN cc_start: 0.8541 (mt0) cc_final: 0.8219 (mm-40) REVERT: A 194 PHE cc_start: 0.8863 (t80) cc_final: 0.8636 (t80) REVERT: A 268 GLU cc_start: 0.8054 (pp20) cc_final: 0.7679 (pp20) REVERT: A 380 MET cc_start: 0.8170 (tpp) cc_final: 0.7603 (tmm) REVERT: A 466 MET cc_start: 0.8697 (tmm) cc_final: 0.8470 (tmm) REVERT: A 482 MET cc_start: 0.7627 (mmm) cc_final: 0.7362 (mmm) REVERT: A 485 MET cc_start: 0.7753 (pmm) cc_final: 0.7488 (pmm) REVERT: A 757 LYS cc_start: 0.8371 (mmpt) cc_final: 0.7839 (mptt) REVERT: A 887 MET cc_start: 0.8710 (tpp) cc_final: 0.8493 (tpp) REVERT: A 928 MET cc_start: 0.8273 (tpp) cc_final: 0.8007 (tpp) REVERT: A 1008 ILE cc_start: 0.9147 (mp) cc_final: 0.8806 (mm) REVERT: B 131 GLU cc_start: 0.6827 (tp30) cc_final: 0.6315 (tp30) outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.1550 time to fit residues: 36.9884 Evaluate side-chains 126 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.0020 chunk 49 optimal weight: 0.0040 chunk 58 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108716 restraints weight = 23053.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109834 restraints weight = 11678.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110080 restraints weight = 9563.375| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7994 Z= 0.183 Angle : 0.702 11.859 10866 Z= 0.361 Chirality : 0.044 0.180 1308 Planarity : 0.005 0.095 1372 Dihedral : 5.407 41.449 1111 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.43 % Favored : 91.37 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.29 (0.27), residues: 1021 helix: 0.99 (0.25), residues: 464 sheet: -1.25 (0.49), residues: 118 loop : -2.91 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.004 0.001 HIS A 265 PHE 0.018 0.001 PHE A 953 TYR 0.006 0.001 TYR B 181 ARG 0.004 0.000 ARG A 705 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.83 seconds wall clock time: 48 minutes 36.71 seconds (2916.71 seconds total)