Starting phenix.real_space_refine on Mon Nov 17 19:06:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a69_6987/11_2025/6a69_6987.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a69_6987/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/6a69_6987/11_2025/6a69_6987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a69_6987/11_2025/6a69_6987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6a69_6987/11_2025/6a69_6987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a69_6987/11_2025/6a69_6987.map" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'ASP:plan': 6, 'ASN:plan1': 5, 'TYR:plan': 2, 'GLU:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 2} 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: 2.23, per 1000 atoms: 0.28 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: 0.39 Conformation dependent library (CDL) restraints added in 365.0 milliseconds 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: 0.19 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: 0.97 Time building geometry restraints manager: 0.57 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.110 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.930 ------------------------------------------------------------------------------- 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 7996 Z= 0.483 Angle : 1.480 14.780 10871 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A 272 TYR 0.032 0.003 TYR A 445 PHE 0.036 0.004 PHE A 953 TRP 0.047 0.004 TRP B 225 HIS 0.009 0.003 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.01075 ( 7994) covalent geometry : angle 1.48034 (10866) SS BOND : bond 0.00490 ( 1) SS BOND : angle 1.29656 ( 2) hydrogen bonds : bond 0.17936 ( 358) hydrogen bonds : angle 7.61429 ( 1038) link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 1.63205 ( 3) *********************** 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 : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8689 (mt-10) REVERT: A 217 GLN cc_start: 0.8337 (tt0) cc_final: 0.7901 (tp40) REVERT: A 235 ASP cc_start: 0.8010 (m-30) cc_final: 0.7797 (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 794 VAL cc_start: 0.9608 (t) cc_final: 0.9408 (p) REVERT: A 814 MET cc_start: 0.8765 (mmp) cc_final: 0.8410 (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: 0.8446 (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: 0.0832 time to fit residues: 27.5848 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 : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106364 restraints weight = 19355.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105260 restraints weight = 13782.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106086 restraints weight = 9864.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106766 restraints weight = 7640.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107131 restraints weight = 6681.343| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7996 Z= 0.156 Angle : 0.813 12.884 10871 Z= 0.421 Chirality : 0.047 0.195 1308 Planarity : 0.007 0.070 1372 Dihedral : 6.970 40.301 1111 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.14 % Favored : 91.67 % Rotamer: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.24), residues: 1021 helix: -0.56 (0.23), residues: 461 sheet: -2.79 (0.42), residues: 113 loop : -3.61 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 558 TYR 0.013 0.001 TYR B 244 PHE 0.026 0.002 PHE A 953 TRP 0.012 0.001 TRP B 225 HIS 0.006 0.001 HIS A 971 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7994) covalent geometry : angle 0.81303 (10866) SS BOND : bond 0.00263 ( 1) SS BOND : angle 0.16262 ( 2) hydrogen bonds : bond 0.05449 ( 358) hydrogen bonds : angle 5.59654 ( 1038) link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 1.48398 ( 3) *********************** 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 219 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.301 Fit side-chains REVERT: A 79 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8152 (mp0) REVERT: A 217 GLN cc_start: 0.8205 (tt0) cc_final: 0.7951 (tp40) REVERT: A 268 GLU cc_start: 0.8209 (pp20) cc_final: 0.7911 (pp20) REVERT: A 421 ILE cc_start: 0.9573 (tp) cc_final: 0.9342 (tp) REVERT: A 466 MET cc_start: 0.8654 (tmm) cc_final: 0.7954 (tmm) REVERT: A 887 MET cc_start: 0.8849 (tpp) cc_final: 0.8469 (tpp) REVERT: A 964 LEU cc_start: 0.8828 (tt) cc_final: 0.8365 (tt) REVERT: A 1006 ASN cc_start: 0.8494 (m-40) cc_final: 0.7716 (m-40) REVERT: B 157 LYS cc_start: 0.6261 (tptp) cc_final: 0.5627 (mmmt) REVERT: B 199 GLU cc_start: 0.5413 (pt0) cc_final: 0.5195 (pt0) outliers start: 2 outliers final: 2 residues processed: 218 average time/residue: 0.0714 time to fit residues: 22.4092 Evaluate side-chains 136 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 81 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 6 optimal weight: 0.0770 chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108626 restraints weight = 19398.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108590 restraints weight = 11213.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109172 restraints weight = 9579.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109806 restraints weight = 7342.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110167 restraints weight = 6581.306| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7996 Z= 0.140 Angle : 0.759 12.627 10871 Z= 0.394 Chirality : 0.046 0.192 1308 Planarity : 0.006 0.087 1372 Dihedral : 6.314 39.351 1111 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.71 % Favored : 90.10 % Rotamer: Outliers : 0.12 % Allowed : 2.65 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.25), residues: 1021 helix: 0.25 (0.24), residues: 455 sheet: -2.52 (0.44), residues: 113 loop : -3.41 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 767 TYR 0.010 0.001 TYR A 445 PHE 0.019 0.001 PHE A 953 TRP 0.007 0.001 TRP A1041 HIS 0.005 0.001 HIS A 971 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7994) covalent geometry : angle 0.75920 (10866) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.41044 ( 2) hydrogen bonds : bond 0.04570 ( 358) hydrogen bonds : angle 5.03103 ( 1038) link_NAG-ASN : bond 0.00334 ( 1) link_NAG-ASN : angle 1.39265 ( 3) *********************** 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 188 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8059 (mp0) REVERT: A 466 MET cc_start: 0.8749 (tmm) cc_final: 0.8061 (tmm) REVERT: A 482 MET cc_start: 0.7806 (mmm) cc_final: 0.7579 (mmm) REVERT: A 928 MET cc_start: 0.8214 (tpp) cc_final: 0.7840 (tpp) REVERT: A 1006 ASN cc_start: 0.8479 (m-40) cc_final: 0.7963 (m-40) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.0721 time to fit residues: 19.5084 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3745 r_free = 0.3745 target = 0.137840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102794 restraints weight = 20374.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102628 restraints weight = 11635.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102750 restraints weight = 11824.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104438 restraints weight = 8362.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104552 restraints weight = 6300.902| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 7996 Z= 0.219 Angle : 0.798 11.989 10871 Z= 0.417 Chirality : 0.047 0.177 1308 Planarity : 0.006 0.086 1372 Dihedral : 6.208 42.622 1111 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.29 % Favored : 89.51 % Rotamer: Outliers : 0.24 % Allowed : 2.90 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.25), residues: 1021 helix: 0.21 (0.24), residues: 465 sheet: -2.29 (0.45), residues: 105 loop : -3.46 (0.24), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 767 TYR 0.020 0.001 TYR A 445 PHE 0.019 0.002 PHE B 227 TRP 0.009 0.001 TRP A 404 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 7994) covalent geometry : angle 0.79768 (10866) SS BOND : bond 0.00102 ( 1) SS BOND : angle 0.63873 ( 2) hydrogen bonds : bond 0.05110 ( 358) hydrogen bonds : angle 5.06169 ( 1038) link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 1.02180 ( 3) *********************** 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 176 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8099 (mp0) REVERT: A 217 GLN cc_start: 0.7940 (pp30) cc_final: 0.7705 (pp30) REVERT: A 268 GLU cc_start: 0.7971 (pp20) cc_final: 0.7708 (pp20) REVERT: A 466 MET cc_start: 0.8771 (tmm) cc_final: 0.8172 (tmm) REVERT: A 482 MET cc_start: 0.7917 (mmm) cc_final: 0.7643 (mmm) REVERT: A 887 MET cc_start: 0.9175 (tpp) cc_final: 0.8412 (tpp) REVERT: A 928 MET cc_start: 0.8285 (tpp) cc_final: 0.8000 (tpp) REVERT: A 998 ASN cc_start: 0.8129 (t0) cc_final: 0.7668 (t0) REVERT: B 131 GLU cc_start: 0.6647 (tp30) cc_final: 0.6340 (tp30) outliers start: 2 outliers final: 1 residues processed: 174 average time/residue: 0.0600 time to fit residues: 15.6389 Evaluate side-chains 125 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 790 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 = 0.3795 r_free = 0.3795 target = 0.141749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105094 restraints weight = 36024.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106080 restraints weight = 15217.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107153 restraints weight = 10773.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107843 restraints weight = 7839.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108334 restraints weight = 6735.646| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7996 Z= 0.140 Angle : 0.739 14.548 10871 Z= 0.383 Chirality : 0.045 0.182 1308 Planarity : 0.006 0.092 1372 Dihedral : 6.036 40.345 1111 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.22 % Favored : 90.59 % Rotamer: Outliers : 0.36 % Allowed : 1.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.26), residues: 1021 helix: 0.60 (0.25), residues: 458 sheet: -2.16 (0.45), residues: 113 loop : -3.23 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 767 TYR 0.008 0.001 TYR A 445 PHE 0.025 0.001 PHE A 953 TRP 0.007 0.001 TRP A 759 HIS 0.008 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7994) covalent geometry : angle 0.73935 (10866) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.44880 ( 2) hydrogen bonds : bond 0.04374 ( 358) hydrogen bonds : angle 4.74895 ( 1038) link_NAG-ASN : bond 0.00210 ( 1) link_NAG-ASN : angle 1.04506 ( 3) *********************** 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 191 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8068 (mp0) REVERT: A 159 ILE cc_start: 0.9245 (mt) cc_final: 0.8952 (tt) REVERT: A 268 GLU cc_start: 0.7829 (pp20) cc_final: 0.7584 (pp20) REVERT: A 466 MET cc_start: 0.8786 (tmm) cc_final: 0.8370 (tmm) REVERT: A 482 MET cc_start: 0.7900 (mmm) cc_final: 0.7604 (mmm) REVERT: A 887 MET cc_start: 0.9121 (tpp) cc_final: 0.8561 (tpp) REVERT: A 928 MET cc_start: 0.8146 (tpp) cc_final: 0.7748 (tpp) REVERT: A 952 LYS cc_start: 0.6128 (mttt) cc_final: 0.5632 (mmtp) REVERT: A 998 ASN cc_start: 0.8135 (t0) cc_final: 0.7763 (t0) REVERT: B 157 LYS cc_start: 0.6508 (tptp) cc_final: 0.5949 (mmmt) outliers start: 3 outliers final: 2 residues processed: 190 average time/residue: 0.0706 time to fit residues: 19.4885 Evaluate side-chains 134 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 60 optimal weight: 0.0170 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN A 752 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 = 0.3824 r_free = 0.3824 target = 0.144465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109593 restraints weight = 19684.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109377 restraints weight = 11517.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109821 restraints weight = 10356.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111660 restraints weight = 7658.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111645 restraints weight = 6002.289| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7996 Z= 0.130 Angle : 0.687 12.146 10871 Z= 0.360 Chirality : 0.044 0.181 1308 Planarity : 0.006 0.092 1372 Dihedral : 5.728 40.574 1111 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.33 % Favored : 91.47 % Rotamer: Outliers : 0.24 % Allowed : 1.45 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.26), residues: 1021 helix: 0.84 (0.25), residues: 450 sheet: -2.02 (0.47), residues: 106 loop : -3.12 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 767 TYR 0.008 0.001 TYR A 445 PHE 0.028 0.001 PHE A 953 TRP 0.004 0.001 TRP A 404 HIS 0.005 0.001 HIS A 971 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7994) covalent geometry : angle 0.68733 (10866) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.50996 ( 2) hydrogen bonds : bond 0.03863 ( 358) hydrogen bonds : angle 4.59101 ( 1038) link_NAG-ASN : bond 0.00298 ( 1) link_NAG-ASN : angle 0.83463 ( 3) *********************** 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 188 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8004 (mp0) REVERT: A 159 ILE cc_start: 0.9083 (mt) cc_final: 0.8880 (tt) REVERT: A 268 GLU cc_start: 0.7992 (pp20) cc_final: 0.7748 (pp20) REVERT: A 466 MET cc_start: 0.8924 (tmm) cc_final: 0.8483 (tmm) REVERT: A 482 MET cc_start: 0.7722 (mmm) cc_final: 0.7501 (mmm) REVERT: A 751 GLU cc_start: 0.8300 (tp30) cc_final: 0.7951 (tm-30) REVERT: A 752 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8673 (pp30) REVERT: A 757 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7837 (mptt) REVERT: A 887 MET cc_start: 0.9134 (tpp) cc_final: 0.8494 (tpp) REVERT: B 141 MET cc_start: 0.5987 (mpp) cc_final: 0.5786 (mpp) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.0669 time to fit residues: 18.6979 Evaluate side-chains 133 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 97 optimal weight: 6.9990 chunk 72 optimal weight: 0.0570 chunk 61 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 857 GLN A 859 GLN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107054 restraints weight = 19472.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106807 restraints weight = 10964.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107053 restraints weight = 11217.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108653 restraints weight = 8010.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108696 restraints weight = 6252.326| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 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 = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7996 Z= 0.146 Angle : 0.693 11.896 10871 Z= 0.364 Chirality : 0.044 0.177 1308 Planarity : 0.006 0.096 1372 Dihedral : 5.603 41.193 1111 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.12 % Favored : 90.78 % Rotamer: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.26), residues: 1021 helix: 0.95 (0.25), residues: 452 sheet: -1.94 (0.47), residues: 106 loop : -3.05 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 767 TYR 0.010 0.001 TYR A 445 PHE 0.020 0.001 PHE A 954 TRP 0.006 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7994) covalent geometry : angle 0.69302 (10866) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.58598 ( 2) hydrogen bonds : bond 0.04057 ( 358) hydrogen bonds : angle 4.53563 ( 1038) link_NAG-ASN : bond 0.00173 ( 1) link_NAG-ASN : angle 0.84492 ( 3) *********************** 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 171 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8043 (mp0) REVERT: A 268 GLU cc_start: 0.7966 (pp20) cc_final: 0.7665 (pp20) REVERT: A 466 MET cc_start: 0.8956 (tmm) cc_final: 0.8447 (tmm) REVERT: A 485 MET cc_start: 0.7802 (pmm) cc_final: 0.7503 (pmm) REVERT: A 757 LYS cc_start: 0.8333 (mmpt) cc_final: 0.7850 (mptt) REVERT: A 859 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8490 (tp40) REVERT: A 887 MET cc_start: 0.9150 (tpp) cc_final: 0.8673 (tpp) REVERT: A 928 MET cc_start: 0.8264 (tpp) cc_final: 0.7959 (tpp) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.0655 time to fit residues: 16.6290 Evaluate side-chains 128 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 87 optimal weight: 0.1980 chunk 4 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 859 GLN ** 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 = 0.143599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107757 restraints weight = 19972.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108985 restraints weight = 11447.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109122 restraints weight = 9493.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109891 restraints weight = 7439.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110088 restraints weight = 6533.553| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7996 Z= 0.135 Angle : 0.691 11.932 10871 Z= 0.362 Chirality : 0.045 0.179 1308 Planarity : 0.006 0.099 1372 Dihedral : 5.536 41.184 1111 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.73 % Favored : 91.18 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.26), residues: 1021 helix: 0.89 (0.25), residues: 459 sheet: -1.84 (0.47), residues: 110 loop : -2.95 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 767 TYR 0.008 0.001 TYR A 445 PHE 0.014 0.001 PHE A 194 TRP 0.006 0.001 TRP A 404 HIS 0.005 0.001 HIS A 971 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7994) covalent geometry : angle 0.69136 (10866) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.59825 ( 2) hydrogen bonds : bond 0.03987 ( 358) hydrogen bonds : angle 4.48389 ( 1038) link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 0.85653 ( 3) *********************** 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 173 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7953 (mp0) REVERT: A 268 GLU cc_start: 0.8104 (pp20) cc_final: 0.7788 (pp20) REVERT: A 466 MET cc_start: 0.8921 (tmm) cc_final: 0.8522 (tmm) REVERT: A 485 MET cc_start: 0.7750 (pmm) cc_final: 0.7438 (pmm) REVERT: A 757 LYS cc_start: 0.8327 (mmpt) cc_final: 0.7834 (mptt) REVERT: A 887 MET cc_start: 0.9137 (tpp) cc_final: 0.8642 (tpp) REVERT: A 928 MET cc_start: 0.8197 (tpp) cc_final: 0.7992 (tpp) REVERT: A 1008 ILE cc_start: 0.9188 (mp) cc_final: 0.8836 (mm) REVERT: B 141 MET cc_start: 0.6495 (mpp) cc_final: 0.6277 (mpp) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.0785 time to fit residues: 19.1319 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 : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 0.0040 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 509 ASN A 711 ASN A 857 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108606 restraints weight = 27575.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109540 restraints weight = 16423.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110051 restraints weight = 13921.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111391 restraints weight = 8960.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112044 restraints weight = 7221.193| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7996 Z= 0.137 Angle : 0.712 11.810 10871 Z= 0.369 Chirality : 0.044 0.178 1308 Planarity : 0.006 0.097 1372 Dihedral : 5.620 40.300 1111 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.12 % Favored : 90.78 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.26), residues: 1021 helix: 0.87 (0.25), residues: 460 sheet: -1.70 (0.46), residues: 117 loop : -2.94 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 767 TYR 0.007 0.001 TYR A 445 PHE 0.036 0.001 PHE A 953 TRP 0.006 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7994) covalent geometry : angle 0.71201 (10866) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.55669 ( 2) hydrogen bonds : bond 0.03954 ( 358) hydrogen bonds : angle 4.50687 ( 1038) link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 0.85829 ( 3) *********************** 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 166 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7950 (mp0) REVERT: A 194 PHE cc_start: 0.8784 (t80) cc_final: 0.8468 (t80) REVERT: A 268 GLU cc_start: 0.8056 (pp20) cc_final: 0.7746 (pp20) REVERT: A 466 MET cc_start: 0.8896 (tmm) cc_final: 0.8512 (tmm) REVERT: A 485 MET cc_start: 0.7710 (pmm) cc_final: 0.7449 (pmm) REVERT: A 706 MET cc_start: 0.8896 (tpp) cc_final: 0.8677 (ttt) REVERT: A 757 LYS cc_start: 0.8342 (mmpt) cc_final: 0.7820 (mptt) REVERT: A 887 MET cc_start: 0.9164 (tpp) cc_final: 0.8700 (tpp) REVERT: A 909 GLU cc_start: 0.8364 (tp30) cc_final: 0.8064 (tp30) REVERT: A 1008 ILE cc_start: 0.9213 (mp) cc_final: 0.8851 (mm) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.0687 time to fit residues: 16.7297 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 : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 99 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN A 859 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110190 restraints weight = 35492.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112745 restraints weight = 22081.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113300 restraints weight = 15628.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114532 restraints weight = 9502.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116584 restraints weight = 7594.171| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7996 Z= 0.132 Angle : 0.715 11.990 10871 Z= 0.370 Chirality : 0.045 0.179 1308 Planarity : 0.006 0.093 1372 Dihedral : 5.546 39.964 1111 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.33 % Favored : 91.57 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.27), residues: 1021 helix: 0.87 (0.25), residues: 462 sheet: -1.47 (0.48), residues: 118 loop : -2.89 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 767 TYR 0.011 0.001 TYR A 497 PHE 0.043 0.001 PHE A 953 TRP 0.005 0.001 TRP A 404 HIS 0.005 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7994) covalent geometry : angle 0.71528 (10866) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.62366 ( 2) hydrogen bonds : bond 0.03806 ( 358) hydrogen bonds : angle 4.42672 ( 1038) link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 0.86609 ( 3) ********************** 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 167 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7892 (mp0) REVERT: A 192 GLN cc_start: 0.8485 (mt0) cc_final: 0.8244 (mm-40) REVERT: A 194 PHE cc_start: 0.8826 (t80) cc_final: 0.8522 (t80) REVERT: A 268 GLU cc_start: 0.8058 (pp20) cc_final: 0.7723 (pp20) REVERT: A 454 ASN cc_start: 0.9040 (m110) cc_final: 0.8838 (m110) REVERT: A 466 MET cc_start: 0.8756 (tmm) cc_final: 0.8433 (tmm) REVERT: A 485 MET cc_start: 0.7685 (pmm) cc_final: 0.7459 (pmm) REVERT: A 757 LYS cc_start: 0.8283 (mmpt) cc_final: 0.7779 (mptt) REVERT: A 826 SER cc_start: 0.9320 (p) cc_final: 0.9104 (p) REVERT: A 887 MET cc_start: 0.9136 (tpp) cc_final: 0.8468 (tpp) REVERT: A 1008 ILE cc_start: 0.9149 (mp) cc_final: 0.8778 (mm) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.0651 time to fit residues: 16.0950 Evaluate side-chains 124 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.0040 chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109884 restraints weight = 29501.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110579 restraints weight = 16925.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111500 restraints weight = 13764.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112405 restraints weight = 9130.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114039 restraints weight = 7550.229| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7996 Z= 0.128 Angle : 0.707 13.873 10871 Z= 0.365 Chirality : 0.044 0.180 1308 Planarity : 0.006 0.091 1372 Dihedral : 5.447 39.555 1111 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.73 % Favored : 91.18 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.27), residues: 1021 helix: 0.93 (0.25), residues: 465 sheet: -1.36 (0.49), residues: 118 loop : -2.82 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 767 TYR 0.009 0.001 TYR A 497 PHE 0.042 0.001 PHE A 953 TRP 0.008 0.001 TRP A1041 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7994) covalent geometry : angle 0.70678 (10866) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.59999 ( 2) hydrogen bonds : bond 0.03721 ( 358) hydrogen bonds : angle 4.36337 ( 1038) link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 0.86315 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1469.67 seconds wall clock time: 26 minutes 0.46 seconds (1560.46 seconds total)