Starting phenix.real_space_refine on Sat Feb 17 03:36:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8t_25745/02_2024/7t8t_25745.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8t_25745/02_2024/7t8t_25745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8t_25745/02_2024/7t8t_25745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8t_25745/02_2024/7t8t_25745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8t_25745/02_2024/7t8t_25745.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8t_25745/02_2024/7t8t_25745.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 49 5.16 5 C 5595 2.51 5 N 1517 2.21 5 O 1646 1.98 5 H 8626 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 679": "OE1" <-> "OE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17434 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 17434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 17434 Unusual residues: {' CA': 1} Classifications: {'peptide': 1086, 'undetermined': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1029, None: 1} Not linked: pdbres="LYS A1215 " pdbres=" CA A1301 " Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 7.78, per 1000 atoms: 0.45 Number of scatterers: 17434 At special positions: 0 Unit cell: (86.45, 103.74, 111.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 49 16.00 O 1646 8.00 N 1517 7.00 C 5595 6.00 H 8626 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.76 Conformation dependent library (CDL) restraints added in 1.7 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 30.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 4.166A pdb=" N GLY A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 4.328A pdb=" N GLU A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 146 removed outlier: 3.848A pdb=" N GLN A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.666A pdb=" N PHE A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.538A pdb=" N VAL A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.811A pdb=" N PHE A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.828A pdb=" N ALA A 316 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 349 through 360 removed outlier: 4.165A pdb=" N TYR A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 360 " --> pdb=" O CYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.725A pdb=" N LYS A 456 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 558 through 568 removed outlier: 4.565A pdb=" N GLU A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 567 " --> pdb=" O HIS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.869A pdb=" N ILE A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 removed outlier: 4.070A pdb=" N TYR A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.737A pdb=" N VAL A 685 " --> pdb=" O MET A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.584A pdb=" N LYS A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 763 Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 915 through 931 removed outlier: 3.605A pdb=" N LEU A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 957 removed outlier: 3.549A pdb=" N SER A 954 " --> pdb=" O ALA A 950 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 956 " --> pdb=" O GLU A 952 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 removed outlier: 3.736A pdb=" N LYS A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1005 removed outlier: 4.679A pdb=" N LYS A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A1002 " --> pdb=" O LYS A 998 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A1004 " --> pdb=" O PHE A1000 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'A' and resid 1044 through 1054 removed outlier: 3.771A pdb=" N PHE A1054 " --> pdb=" O ASN A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1071 Processing helix chain 'A' and resid 1078 through 1083 removed outlier: 3.519A pdb=" N ARG A1083 " --> pdb=" O SER A1080 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 3.739A pdb=" N THR A 50 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 121 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N CYS A 106 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 108 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE A 81 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU A 110 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.767A pdb=" N PHE A 293 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.445A pdb=" N ILE A 364 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU A 414 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A 366 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 409 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LYS A 462 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 411 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 491 through 497 removed outlier: 3.627A pdb=" N LYS A 491 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A 509 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 519 " --> pdb=" O GLY A 874 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 583 through 587 removed outlier: 3.858A pdb=" N PHE A 599 " --> pdb=" O GLN A 606 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 610 through 611 Processing sheet with id=AA7, first strand: chain 'A' and resid 723 through 725 removed outlier: 4.673A pdb=" N ALA A 690 " --> pdb=" O ARG A 707 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA9, first strand: chain 'A' and resid 982 through 983 Processing sheet with id=AB1, first strand: chain 'A' and resid 1145 through 1149 removed outlier: 7.027A pdb=" N LEU A1206 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA A1097 " --> pdb=" O SER A1204 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A1204 " --> pdb=" O ALA A1097 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1124 through 1127 removed outlier: 3.823A pdb=" N ALA A1174 " --> pdb=" O VAL A1161 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU A1163 " --> pdb=" O PHE A1172 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A1172 " --> pdb=" O GLU A1163 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 726 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: 6.57 Time building geometry restraints manager: 14.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8606 1.03 - 1.23: 21 1.23 - 1.42: 3836 1.42 - 1.61: 5098 1.61 - 1.81: 78 Bond restraints: 17639 Sorted by residual: bond pdb=" CB TRP A 668 " pdb=" CG TRP A 668 " ideal model delta sigma weight residual 1.498 1.529 -0.031 3.10e-02 1.04e+03 1.02e+00 bond pdb=" CA PRO A 984 " pdb=" C PRO A 984 " ideal model delta sigma weight residual 1.520 1.532 -0.013 1.42e-02 4.96e+03 7.82e-01 bond pdb=" C GLU A 768 " pdb=" N PRO A 769 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.44e-02 4.82e+03 7.14e-01 bond pdb=" CA PRO A 984 " pdb=" CB PRO A 984 " ideal model delta sigma weight residual 1.533 1.522 0.012 1.42e-02 4.96e+03 6.73e-01 bond pdb=" C PHE A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.20e-01 ... (remaining 17634 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.85: 166 104.85 - 112.25: 19936 112.25 - 119.64: 4747 119.64 - 127.04: 6864 127.04 - 134.43: 118 Bond angle restraints: 31831 Sorted by residual: angle pdb=" N VAL A 164 " pdb=" CA VAL A 164 " pdb=" C VAL A 164 " ideal model delta sigma weight residual 111.91 108.73 3.18 8.90e-01 1.26e+00 1.27e+01 angle pdb=" CB ARG A 423 " pdb=" CG ARG A 423 " pdb=" CD ARG A 423 " ideal model delta sigma weight residual 111.30 118.61 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" N ASP A1122 " pdb=" CA ASP A1122 " pdb=" C ASP A1122 " ideal model delta sigma weight residual 114.04 110.53 3.51 1.24e+00 6.50e-01 8.00e+00 angle pdb=" C GLU A 474 " pdb=" N VAL A 475 " pdb=" CA VAL A 475 " ideal model delta sigma weight residual 122.13 127.31 -5.18 1.85e+00 2.92e-01 7.83e+00 angle pdb=" N ARG A 423 " pdb=" CA ARG A 423 " pdb=" CB ARG A 423 " ideal model delta sigma weight residual 110.12 114.01 -3.89 1.47e+00 4.63e-01 7.00e+00 ... (remaining 31826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 7550 17.19 - 34.38: 582 34.38 - 51.58: 155 51.58 - 68.77: 36 68.77 - 85.96: 9 Dihedral angle restraints: 8332 sinusoidal: 4520 harmonic: 3812 Sorted by residual: dihedral pdb=" CA LEU A 194 " pdb=" C LEU A 194 " pdb=" N ARG A 195 " pdb=" CA ARG A 195 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ARG A 945 " pdb=" C ARG A 945 " pdb=" N ARG A 946 " pdb=" CA ARG A 946 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU A 289 " pdb=" C GLU A 289 " pdb=" N GLU A 290 " pdb=" CA GLU A 290 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 8329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 910 0.032 - 0.065: 267 0.065 - 0.097: 72 0.097 - 0.129: 56 0.129 - 0.162: 2 Chirality restraints: 1307 Sorted by residual: chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ILE A 109 " pdb=" N ILE A 109 " pdb=" C ILE A 109 " pdb=" CB ILE A 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A1011 " pdb=" N ILE A1011 " pdb=" C ILE A1011 " pdb=" CB ILE A1011 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1304 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 985 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C GLU A 985 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU A 985 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 986 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 668 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C TRP A 668 " 0.025 2.00e-02 2.50e+03 pdb=" O TRP A 668 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 669 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 423 " 0.097 9.50e-02 1.11e+02 3.27e-02 1.71e+00 pdb=" NE ARG A 423 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 423 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 423 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 423 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG A 423 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 423 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 423 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 423 " 0.001 2.00e-02 2.50e+03 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1151 2.20 - 2.80: 35642 2.80 - 3.40: 44872 3.40 - 4.00: 58252 4.00 - 4.60: 88840 Nonbonded interactions: 228757 Sorted by model distance: nonbonded pdb=" OD1 ASP A 342 " pdb=" HG SER A 346 " model vdw 1.602 1.850 nonbonded pdb=" H SER A 588 " pdb=" O ASP A 594 " model vdw 1.616 1.850 nonbonded pdb=" OD1 ASN A 993 " pdb=" H LYS A 996 " model vdw 1.618 1.850 nonbonded pdb=" OD1 ASP A1165 " pdb=" H ASP A1169 " model vdw 1.619 1.850 nonbonded pdb=" HG SER A 915 " pdb=" OE1 GLU A 918 " model vdw 1.621 1.850 ... (remaining 228752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.250 Extract box with map and model: 5.520 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 56.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.002 0.031 9013 Z= 0.145 Angle : 0.500 7.309 12185 Z= 0.270 Chirality : 0.039 0.162 1307 Planarity : 0.003 0.042 1584 Dihedral : 13.832 85.961 3402 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 1074 helix: 1.32 (0.35), residues: 264 sheet: -0.66 (0.35), residues: 231 loop : -1.40 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 550 HIS 0.002 0.000 HIS A 508 PHE 0.014 0.001 PHE A 254 TYR 0.006 0.001 TYR A1012 ARG 0.012 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3767 time to fit residues: 40.9463 Evaluate side-chains 62 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 503 HIS A 545 HIS ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 9013 Z= 0.379 Angle : 0.601 5.482 12185 Z= 0.319 Chirality : 0.042 0.145 1307 Planarity : 0.005 0.045 1584 Dihedral : 4.518 18.067 1193 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.78 % Favored : 90.04 % Rotamer: Outliers : 0.31 % Allowed : 4.76 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.26), residues: 1074 helix: 0.80 (0.33), residues: 267 sheet: -0.86 (0.34), residues: 226 loop : -1.85 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 550 HIS 0.005 0.001 HIS A1099 PHE 0.020 0.002 PHE A 276 TYR 0.010 0.002 TYR A 379 ARG 0.006 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8126 (tmtt) cc_final: 0.7896 (ptpt) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.4245 time to fit residues: 37.9708 Evaluate side-chains 57 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9013 Z= 0.132 Angle : 0.476 5.920 12185 Z= 0.246 Chirality : 0.039 0.134 1307 Planarity : 0.004 0.063 1584 Dihedral : 4.081 17.174 1193 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 0.31 % Allowed : 5.18 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 1074 helix: 1.04 (0.34), residues: 275 sheet: -0.69 (0.34), residues: 235 loop : -1.68 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 668 HIS 0.003 0.001 HIS A 508 PHE 0.009 0.001 PHE A 276 TYR 0.009 0.001 TYR A 519 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.7356 (tmm) cc_final: 0.7055 (tmm) REVERT: A 305 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7865 (ptpt) REVERT: A 571 GLU cc_start: 0.8496 (mp0) cc_final: 0.8260 (pm20) REVERT: A 651 MET cc_start: 0.4169 (mmp) cc_final: 0.3909 (mmp) outliers start: 3 outliers final: 2 residues processed: 66 average time/residue: 0.3814 time to fit residues: 38.1778 Evaluate side-chains 62 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 1112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9013 Z= 0.226 Angle : 0.499 5.828 12185 Z= 0.261 Chirality : 0.039 0.138 1307 Planarity : 0.004 0.058 1584 Dihedral : 4.175 17.567 1193 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.22 % Favored : 90.60 % Rotamer: Outliers : 0.41 % Allowed : 6.52 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.26), residues: 1074 helix: 0.99 (0.34), residues: 275 sheet: -0.78 (0.34), residues: 235 loop : -1.78 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1140 HIS 0.004 0.001 HIS A 508 PHE 0.013 0.001 PHE A 276 TYR 0.011 0.001 TYR A 519 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.7321 (tmm) cc_final: 0.7045 (tmm) REVERT: A 305 LYS cc_start: 0.8087 (tmtt) cc_final: 0.7878 (ptpt) REVERT: A 571 GLU cc_start: 0.8463 (mp0) cc_final: 0.8219 (pm20) REVERT: A 651 MET cc_start: 0.4171 (mmp) cc_final: 0.3910 (mmp) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.3957 time to fit residues: 37.4926 Evaluate side-chains 59 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9013 Z= 0.280 Angle : 0.538 5.919 12185 Z= 0.283 Chirality : 0.040 0.141 1307 Planarity : 0.004 0.054 1584 Dihedral : 4.452 18.046 1193 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.15 % Favored : 89.66 % Rotamer: Outliers : 0.72 % Allowed : 8.07 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.26), residues: 1074 helix: 0.91 (0.34), residues: 269 sheet: -0.88 (0.34), residues: 228 loop : -1.90 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1140 HIS 0.005 0.001 HIS A 508 PHE 0.016 0.002 PHE A 276 TYR 0.013 0.001 TYR A 754 ARG 0.005 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 GLU cc_start: 0.8430 (mp0) cc_final: 0.8195 (pm20) REVERT: A 651 MET cc_start: 0.3844 (mmp) cc_final: 0.3626 (mmp) REVERT: A 1047 MET cc_start: 0.8637 (tpp) cc_final: 0.8417 (tpt) outliers start: 7 outliers final: 7 residues processed: 61 average time/residue: 0.4118 time to fit residues: 37.5741 Evaluate side-chains 60 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 GLU Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9013 Z= 0.180 Angle : 0.492 6.459 12185 Z= 0.255 Chirality : 0.039 0.139 1307 Planarity : 0.004 0.053 1584 Dihedral : 4.231 17.528 1193 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.19 % Favored : 91.62 % Rotamer: Outliers : 0.62 % Allowed : 8.28 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1074 helix: 1.10 (0.34), residues: 269 sheet: -0.82 (0.34), residues: 231 loop : -1.84 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 668 HIS 0.004 0.001 HIS A 508 PHE 0.012 0.001 PHE A 276 TYR 0.011 0.001 TYR A 519 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.7984 (tptt) cc_final: 0.7723 (pttt) REVERT: A 651 MET cc_start: 0.3820 (mmp) cc_final: 0.3515 (mmp) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.4293 time to fit residues: 40.4509 Evaluate side-chains 61 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9013 Z= 0.222 Angle : 0.508 6.951 12185 Z= 0.264 Chirality : 0.039 0.140 1307 Planarity : 0.004 0.052 1584 Dihedral : 4.281 18.202 1193 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.87 % Favored : 89.94 % Rotamer: Outliers : 1.04 % Allowed : 8.07 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 1074 helix: 1.13 (0.34), residues: 269 sheet: -0.89 (0.34), residues: 228 loop : -1.86 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1140 HIS 0.004 0.001 HIS A 508 PHE 0.013 0.001 PHE A 276 TYR 0.011 0.001 TYR A 519 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.7903 (tptt) cc_final: 0.7682 (pttt) REVERT: A 651 MET cc_start: 0.3522 (mmp) cc_final: 0.3180 (mmp) REVERT: A 1047 MET cc_start: 0.8597 (tpp) cc_final: 0.8388 (tpt) outliers start: 10 outliers final: 10 residues processed: 67 average time/residue: 0.4462 time to fit residues: 43.7368 Evaluate side-chains 64 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 GLU Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9013 Z= 0.130 Angle : 0.471 6.746 12185 Z= 0.241 Chirality : 0.039 0.137 1307 Planarity : 0.004 0.053 1584 Dihedral : 3.998 17.524 1193 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.61 % Favored : 93.20 % Rotamer: Outliers : 0.52 % Allowed : 8.59 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 1074 helix: 1.27 (0.34), residues: 275 sheet: -0.77 (0.34), residues: 231 loop : -1.74 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 668 HIS 0.003 0.000 HIS A 508 PHE 0.008 0.001 PHE A 276 TYR 0.010 0.001 TYR A 519 ARG 0.002 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8034 (tptt) cc_final: 0.7767 (pttt) REVERT: A 651 MET cc_start: 0.3399 (mmp) cc_final: 0.3073 (mmp) outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.4187 time to fit residues: 39.0493 Evaluate side-chains 62 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 42 optimal weight: 0.0970 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9013 Z= 0.135 Angle : 0.470 6.476 12185 Z= 0.240 Chirality : 0.039 0.136 1307 Planarity : 0.004 0.053 1584 Dihedral : 3.922 17.579 1193 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.54 % Favored : 92.27 % Rotamer: Outliers : 0.62 % Allowed : 8.59 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.27), residues: 1074 helix: 1.45 (0.34), residues: 269 sheet: -0.69 (0.35), residues: 231 loop : -1.64 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 668 HIS 0.004 0.000 HIS A 508 PHE 0.009 0.001 PHE A1111 TYR 0.011 0.001 TYR A 519 ARG 0.002 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8030 (tptt) cc_final: 0.7762 (pttt) REVERT: A 651 MET cc_start: 0.3421 (mmp) cc_final: 0.3102 (mmp) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.4126 time to fit residues: 38.8996 Evaluate side-chains 64 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9013 Z= 0.257 Angle : 0.522 6.183 12185 Z= 0.273 Chirality : 0.040 0.140 1307 Planarity : 0.004 0.054 1584 Dihedral : 4.225 18.461 1193 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.78 % Favored : 90.04 % Rotamer: Outliers : 0.62 % Allowed : 8.70 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.26), residues: 1074 helix: 1.24 (0.34), residues: 269 sheet: -0.89 (0.34), residues: 228 loop : -1.82 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1140 HIS 0.004 0.001 HIS A 508 PHE 0.013 0.001 PHE A 276 TYR 0.012 0.001 TYR A 572 ARG 0.001 0.000 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.3304 (mmp) cc_final: 0.3013 (mmp) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.4175 time to fit residues: 40.1789 Evaluate side-chains 61 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 HIS ** 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 = 0.4070 r_free = 0.4070 target = 0.125743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089943 restraints weight = 57000.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.094260 restraints weight = 24272.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096924 restraints weight = 14940.688| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9013 Z= 0.127 Angle : 0.475 6.409 12185 Z= 0.242 Chirality : 0.039 0.136 1307 Planarity : 0.004 0.053 1584 Dihedral : 3.970 17.432 1193 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.89 % Favored : 92.92 % Rotamer: Outliers : 0.72 % Allowed : 8.59 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.27), residues: 1074 helix: 1.42 (0.34), residues: 269 sheet: -0.75 (0.34), residues: 231 loop : -1.66 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 668 HIS 0.004 0.000 HIS A 508 PHE 0.008 0.001 PHE A 280 TYR 0.011 0.001 TYR A 572 ARG 0.002 0.000 ARG A 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.69 seconds wall clock time: 60 minutes 40.22 seconds (3640.22 seconds total)