Starting phenix.real_space_refine on Tue Feb 11 15:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z52_14513/02_2025/7z52_14513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z52_14513/02_2025/7z52_14513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z52_14513/02_2025/7z52_14513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z52_14513/02_2025/7z52_14513.map" model { file = "/net/cci-nas-00/data/ceres_data/7z52_14513/02_2025/7z52_14513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z52_14513/02_2025/7z52_14513.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 45 5.16 5 C 3731 2.51 5 N 1002 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5911 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5494 Classifications: {'peptide': 706} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 680} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "A" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 290 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 36} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.07, per 1000 atoms: 0.69 Number of scatterers: 5911 At special positions: 0 Unit cell: (87.6736, 88.5248, 77.4592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 7 15.00 O 1126 8.00 N 1002 7.00 C 3731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 781.6 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 50.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 162 through 166 removed outlier: 4.065A pdb=" N GLY B 166 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 181 removed outlier: 4.528A pdb=" N ALA B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.748A pdb=" N GLU B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 238 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.807A pdb=" N GLU B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.676A pdb=" N PHE B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.637A pdb=" N PHE B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.504A pdb=" N ILE B 377 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 407 removed outlier: 3.546A pdb=" N CYS B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 430 removed outlier: 3.889A pdb=" N ASN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 removed outlier: 4.135A pdb=" N ASP B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 431 through 436' Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.690A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 460 through 474 removed outlier: 3.636A pdb=" N GLU B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 removed outlier: 3.535A pdb=" N ALA B 486 " --> pdb=" O GLU B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 580 through 587 removed outlier: 3.656A pdb=" N MET B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 Processing helix chain 'B' and resid 832 through 843 removed outlier: 3.998A pdb=" N ARG B 843 " --> pdb=" O LEU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 862 Processing helix chain 'B' and resid 871 through 878 removed outlier: 3.617A pdb=" N VAL B 876 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 895 Processing helix chain 'B' and resid 902 through 907 Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 925 through 948 Proline residue: B 931 - end of helix removed outlier: 3.528A pdb=" N VAL B 945 " --> pdb=" O ARG B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 962 removed outlier: 4.008A pdb=" N PHE B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 974 Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 989 through 1012 removed outlier: 3.540A pdb=" N GLN B1009 " --> pdb=" O ARG B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1029 removed outlier: 3.600A pdb=" N PHE B1023 " --> pdb=" O LEU B1019 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B1024 " --> pdb=" O GLU B1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 668 removed outlier: 3.641A pdb=" N PHE A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.674A pdb=" N LEU A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 99 through 101 removed outlier: 6.765A pdb=" N VAL B 157 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER B 283 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 159 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG B 184 " --> pdb=" O TRP B 248 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ILE B 250 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 186 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY B 210 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR B 228 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N MET B 212 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 332 removed outlier: 7.003A pdb=" N HIS B 318 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 496 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET B 538 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE B 498 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 390 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 389 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA B 481 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 391 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY B 453 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 502 through 504 245 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.71 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: 1865 1.34 - 1.45: 784 1.45 - 1.57: 3293 1.57 - 1.69: 13 1.69 - 1.81: 75 Bond restraints: 6030 Sorted by residual: bond pdb=" O3A ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" O5' ANP B2001 " pdb=" PA ANP B2001 " ideal model delta sigma weight residual 1.655 1.580 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.03e+00 bond pdb=" N GLN B 387 " pdb=" CA GLN B 387 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.44e-02 4.82e+03 7.41e+00 bond pdb=" O2B ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.87e+00 ... (remaining 6025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 8039 2.17 - 4.35: 116 4.35 - 6.52: 16 6.52 - 8.69: 5 8.69 - 10.87: 1 Bond angle restraints: 8177 Sorted by residual: angle pdb=" N VAL B 601 " pdb=" CA VAL B 601 " pdb=" C VAL B 601 " ideal model delta sigma weight residual 112.96 107.96 5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" C HIS B 300 " pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" O1B ANP B2001 " pdb=" PB ANP B2001 " pdb=" O2B ANP B2001 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N PRO B 97 " pdb=" CD PRO B 97 " pdb=" CG PRO B 97 " ideal model delta sigma weight residual 103.20 98.02 5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO B 97 " pdb=" N PRO B 97 " pdb=" CD PRO B 97 " ideal model delta sigma weight residual 112.00 107.53 4.47 1.40e+00 5.10e-01 1.02e+01 ... (remaining 8172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 3609 34.88 - 69.75: 79 69.75 - 104.63: 8 104.63 - 139.50: 1 139.50 - 174.38: 1 Dihedral angle restraints: 3698 sinusoidal: 1518 harmonic: 2180 Sorted by residual: dihedral pdb=" O4' U R 1 " pdb=" C1' U R 1 " pdb=" N1 U R 1 " pdb=" C2 U R 1 " ideal model delta sinusoidal sigma weight residual -128.00 46.38 -174.38 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U R 2 " pdb=" C1' U R 2 " pdb=" N1 U R 2 " pdb=" C2 U R 2 " ideal model delta sinusoidal sigma weight residual -160.00 -54.47 -105.53 1 1.50e+01 4.44e-03 5.41e+01 dihedral pdb=" CA GLN B1009 " pdb=" C GLN B1009 " pdb=" N ALA B1010 " pdb=" CA ALA B1010 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 3695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 759 0.054 - 0.107: 156 0.107 - 0.161: 22 0.161 - 0.215: 0 0.215 - 0.268: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" C3' ANP B2001 " pdb=" C2' ANP B2001 " pdb=" C4' ANP B2001 " pdb=" O3' ANP B2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA VAL B 185 " pdb=" N VAL B 185 " pdb=" C VAL B 185 " pdb=" CB VAL B 185 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE B 139 " pdb=" N ILE B 139 " pdb=" C ILE B 139 " pdb=" CB ILE B 139 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 935 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 921 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO B 922 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 922 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 922 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 560 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ASN B 560 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN B 560 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 561 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 598 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 599 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 599 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 599 " -0.022 5.00e-02 4.00e+02 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 615 2.75 - 3.29: 5722 3.29 - 3.82: 9193 3.82 - 4.36: 11169 4.36 - 4.90: 19323 Nonbonded interactions: 46022 Sorted by model distance: nonbonded pdb=" O LEU B 404 " pdb=" OG1 THR B 407 " model vdw 2.209 3.040 nonbonded pdb=" O THR B 972 " pdb=" OG1 THR B 975 " model vdw 2.269 3.040 nonbonded pdb=" NE2 GLN B 144 " pdb=" O GLY B 166 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASN B 572 " pdb=" NH2 ARG B 575 " model vdw 2.290 3.120 nonbonded pdb=" NZ LYS B 167 " pdb=" O SER B 283 " model vdw 2.291 3.120 ... (remaining 46017 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.870 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 6030 Z= 0.287 Angle : 0.660 10.868 8177 Z= 0.348 Chirality : 0.043 0.268 938 Planarity : 0.004 0.049 1033 Dihedral : 15.636 174.376 2280 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.76 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.69 (0.30), residues: 738 helix: -0.40 (0.28), residues: 362 sheet: 0.44 (0.60), residues: 82 loop : -2.51 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 266 HIS 0.003 0.001 HIS B 456 PHE 0.015 0.002 PHE B 563 TYR 0.011 0.001 TYR B 590 ARG 0.005 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 TYR cc_start: 0.8664 (t80) cc_final: 0.8450 (t80) REVERT: B 244 ARG cc_start: 0.6399 (ttm-80) cc_final: 0.6030 (tpp-160) REVERT: B 256 TYR cc_start: 0.6257 (m-80) cc_final: 0.6005 (m-80) REVERT: B 569 MET cc_start: 0.8217 (ttm) cc_final: 0.7885 (ttm) REVERT: B 590 TYR cc_start: 0.8272 (t80) cc_final: 0.7560 (t80) REVERT: B 935 MET cc_start: 0.8169 (tmm) cc_final: 0.7894 (tmm) REVERT: B 987 ASP cc_start: 0.7078 (p0) cc_final: 0.6339 (p0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1999 time to fit residues: 31.0866 Evaluate side-chains 71 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 207 GLN B 255 HIS B 291 GLN ** B 965 HIS ** 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 = 0.3594 r_free = 0.3594 target = 0.135754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109382 restraints weight = 7319.868| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.09 r_work: 0.3118 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6030 Z= 0.226 Angle : 0.574 9.822 8177 Z= 0.295 Chirality : 0.042 0.140 938 Planarity : 0.004 0.036 1033 Dihedral : 11.509 173.117 907 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.67 % Favored : 91.19 % Rotamer: Outliers : 1.80 % Allowed : 7.86 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.20 (0.30), residues: 738 helix: 0.21 (0.28), residues: 357 sheet: 0.46 (0.62), residues: 83 loop : -2.47 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 266 HIS 0.003 0.001 HIS B 456 PHE 0.012 0.002 PHE B 504 TYR 0.011 0.001 TYR B 319 ARG 0.003 0.001 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: B 120 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7180 (tm-30) REVERT: B 203 TYR cc_start: 0.8867 (t80) cc_final: 0.8655 (t80) REVERT: B 440 GLN cc_start: 0.7119 (mp10) cc_final: 0.6657 (tp40) REVERT: B 569 MET cc_start: 0.8651 (ttm) cc_final: 0.8433 (ttm) REVERT: B 590 TYR cc_start: 0.8701 (t80) cc_final: 0.7644 (t80) REVERT: B 872 MET cc_start: 0.8142 (tpp) cc_final: 0.7857 (tpp) REVERT: B 1042 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8165 (mp) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.1880 time to fit residues: 20.2377 Evaluate side-chains 79 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain A residue 663 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN ** B 965 HIS ** 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 = 0.3556 r_free = 0.3556 target = 0.131794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105702 restraints weight = 7646.066| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.08 r_work: 0.3096 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6030 Z= 0.226 Angle : 0.549 9.705 8177 Z= 0.283 Chirality : 0.042 0.148 938 Planarity : 0.003 0.032 1033 Dihedral : 11.453 173.700 907 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.28 % Rotamer: Outliers : 2.29 % Allowed : 10.15 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.99 (0.31), residues: 738 helix: 0.36 (0.28), residues: 365 sheet: 0.50 (0.61), residues: 83 loop : -2.38 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 266 HIS 0.003 0.001 HIS B 300 PHE 0.010 0.001 PHE B 563 TYR 0.010 0.001 TYR B 319 ARG 0.003 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.644 Fit side-chains REVERT: B 120 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7189 (tm-30) REVERT: B 440 GLN cc_start: 0.7168 (mp10) cc_final: 0.6753 (tp40) REVERT: B 590 TYR cc_start: 0.8835 (t80) cc_final: 0.7790 (t80) REVERT: B 1042 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8244 (mp) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 0.1728 time to fit residues: 18.5645 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain A residue 663 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 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 = 0.3508 r_free = 0.3508 target = 0.128093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102250 restraints weight = 7815.039| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.07 r_work: 0.3028 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6030 Z= 0.326 Angle : 0.608 10.399 8177 Z= 0.312 Chirality : 0.044 0.143 938 Planarity : 0.004 0.031 1033 Dihedral : 11.591 172.141 907 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.33 % Rotamer: Outliers : 3.27 % Allowed : 11.13 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.01 (0.31), residues: 738 helix: 0.39 (0.28), residues: 364 sheet: 0.24 (0.61), residues: 83 loop : -2.36 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 266 HIS 0.006 0.001 HIS B 255 PHE 0.018 0.002 PHE B 563 TYR 0.019 0.002 TYR B 203 ARG 0.006 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.671 Fit side-chains REVERT: B 120 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7313 (tm-30) REVERT: B 440 GLN cc_start: 0.7319 (mp10) cc_final: 0.6885 (tp40) REVERT: B 590 TYR cc_start: 0.8888 (t80) cc_final: 0.7786 (t80) REVERT: B 867 SER cc_start: 0.8287 (m) cc_final: 0.7720 (t) REVERT: B 1031 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8746 (mtpp) REVERT: B 1042 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8290 (mp) outliers start: 20 outliers final: 13 residues processed: 80 average time/residue: 0.1579 time to fit residues: 17.5565 Evaluate side-chains 79 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 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 = 0.3557 r_free = 0.3557 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106272 restraints weight = 7640.226| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.07 r_work: 0.3087 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6030 Z= 0.190 Angle : 0.530 9.018 8177 Z= 0.272 Chirality : 0.041 0.139 938 Planarity : 0.003 0.033 1033 Dihedral : 11.419 172.323 907 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.45 % Favored : 92.41 % Rotamer: Outliers : 3.27 % Allowed : 12.60 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.75 (0.31), residues: 738 helix: 0.65 (0.28), residues: 365 sheet: 0.31 (0.61), residues: 83 loop : -2.30 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 511 HIS 0.003 0.001 HIS B 456 PHE 0.009 0.001 PHE B 143 TYR 0.007 0.001 TYR B 319 ARG 0.002 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.700 Fit side-chains REVERT: B 120 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7213 (tm-30) REVERT: B 440 GLN cc_start: 0.7196 (mp10) cc_final: 0.6791 (tp40) REVERT: B 590 TYR cc_start: 0.8851 (t80) cc_final: 0.7794 (t80) REVERT: B 867 SER cc_start: 0.8198 (m) cc_final: 0.7636 (t) outliers start: 20 outliers final: 10 residues processed: 74 average time/residue: 0.1554 time to fit residues: 16.2422 Evaluate side-chains 73 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 3 optimal weight: 0.0050 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.7976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 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 = 0.3545 r_free = 0.3545 target = 0.131282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105753 restraints weight = 7566.546| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.05 r_work: 0.3081 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6030 Z= 0.199 Angle : 0.511 9.291 8177 Z= 0.264 Chirality : 0.041 0.138 938 Planarity : 0.003 0.033 1033 Dihedral : 11.244 167.180 907 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 3.27 % Allowed : 12.93 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.61 (0.31), residues: 738 helix: 0.77 (0.28), residues: 365 sheet: 0.45 (0.61), residues: 82 loop : -2.25 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 511 HIS 0.003 0.001 HIS B 300 PHE 0.013 0.001 PHE B 504 TYR 0.008 0.001 TYR B 319 ARG 0.001 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.654 Fit side-chains REVERT: B 440 GLN cc_start: 0.7258 (mp10) cc_final: 0.6888 (tp40) REVERT: B 590 TYR cc_start: 0.8861 (t80) cc_final: 0.7826 (t80) REVERT: B 867 SER cc_start: 0.8188 (m) cc_final: 0.7618 (t) outliers start: 20 outliers final: 14 residues processed: 77 average time/residue: 0.1682 time to fit residues: 18.4971 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 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 = 0.3535 r_free = 0.3535 target = 0.130411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104839 restraints weight = 7635.371| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.06 r_work: 0.3058 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6030 Z= 0.221 Angle : 0.528 9.325 8177 Z= 0.272 Chirality : 0.041 0.138 938 Planarity : 0.003 0.033 1033 Dihedral : 11.300 169.543 907 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.99 % Favored : 91.87 % Rotamer: Outliers : 3.11 % Allowed : 13.58 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.63 (0.31), residues: 738 helix: 0.76 (0.28), residues: 365 sheet: 0.42 (0.62), residues: 82 loop : -2.27 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 266 HIS 0.004 0.001 HIS B 300 PHE 0.011 0.001 PHE B 504 TYR 0.009 0.001 TYR B 319 ARG 0.002 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.731 Fit side-chains REVERT: B 440 GLN cc_start: 0.7304 (mp10) cc_final: 0.6920 (tp40) REVERT: B 590 TYR cc_start: 0.8874 (t80) cc_final: 0.7777 (t80) REVERT: B 867 SER cc_start: 0.8202 (m) cc_final: 0.7643 (t) outliers start: 19 outliers final: 15 residues processed: 73 average time/residue: 0.1392 time to fit residues: 14.9932 Evaluate side-chains 76 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 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 = 0.3504 r_free = 0.3504 target = 0.128011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102396 restraints weight = 7704.708| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.08 r_work: 0.3025 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6030 Z= 0.289 Angle : 0.574 10.089 8177 Z= 0.296 Chirality : 0.043 0.139 938 Planarity : 0.003 0.032 1033 Dihedral : 11.476 169.339 907 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.99 % Favored : 91.87 % Rotamer: Outliers : 3.60 % Allowed : 13.42 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.31), residues: 738 helix: 0.66 (0.28), residues: 365 sheet: 1.07 (0.65), residues: 71 loop : -2.36 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 266 HIS 0.005 0.001 HIS B 300 PHE 0.014 0.002 PHE B 563 TYR 0.021 0.001 TYR B 203 ARG 0.003 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.777 Fit side-chains REVERT: B 266 TRP cc_start: 0.7888 (OUTLIER) cc_final: 0.6721 (t-100) REVERT: B 440 GLN cc_start: 0.7324 (mp10) cc_final: 0.6941 (tp40) REVERT: B 590 TYR cc_start: 0.8888 (t80) cc_final: 0.7769 (t80) REVERT: B 867 SER cc_start: 0.8285 (m) cc_final: 0.7740 (t) outliers start: 22 outliers final: 16 residues processed: 77 average time/residue: 0.1353 time to fit residues: 15.1201 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 266 TRP Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 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 = 0.3543 r_free = 0.3543 target = 0.131102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105701 restraints weight = 7646.892| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.06 r_work: 0.3077 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6030 Z= 0.183 Angle : 0.522 10.843 8177 Z= 0.267 Chirality : 0.041 0.135 938 Planarity : 0.003 0.034 1033 Dihedral : 11.274 169.660 907 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.28 % Rotamer: Outliers : 2.62 % Allowed : 14.57 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.50 (0.31), residues: 738 helix: 0.86 (0.29), residues: 365 sheet: 1.30 (0.64), residues: 70 loop : -2.33 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 295 HIS 0.003 0.001 HIS B 300 PHE 0.009 0.001 PHE B 504 TYR 0.007 0.001 TYR B 199 ARG 0.002 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.657 Fit side-chains REVERT: B 266 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6423 (t-100) REVERT: B 385 ASN cc_start: 0.8473 (m-40) cc_final: 0.7978 (t0) REVERT: B 440 GLN cc_start: 0.7276 (mp10) cc_final: 0.6942 (tp40) REVERT: B 590 TYR cc_start: 0.8850 (t80) cc_final: 0.7794 (t80) REVERT: B 867 SER cc_start: 0.8188 (m) cc_final: 0.7637 (t) REVERT: B 956 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6829 (mm-30) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.1474 time to fit residues: 15.9164 Evaluate side-chains 74 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 266 TRP Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 975 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN ** B 965 HIS ** 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 = 0.3576 r_free = 0.3576 target = 0.133763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108185 restraints weight = 7653.086| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.09 r_work: 0.3106 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6030 Z= 0.152 Angle : 0.500 10.623 8177 Z= 0.255 Chirality : 0.040 0.135 938 Planarity : 0.003 0.034 1033 Dihedral : 11.031 171.235 907 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 2.13 % Allowed : 15.55 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.32 (0.32), residues: 738 helix: 1.04 (0.29), residues: 365 sheet: 1.44 (0.64), residues: 70 loop : -2.30 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 295 HIS 0.002 0.001 HIS B 443 PHE 0.014 0.001 PHE B1036 TYR 0.005 0.001 TYR B 311 ARG 0.004 0.000 ARG B 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.621 Fit side-chains REVERT: B 244 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6898 (ttm-80) REVERT: B 266 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.6367 (t-100) REVERT: B 385 ASN cc_start: 0.8389 (m-40) cc_final: 0.7893 (t0) REVERT: B 440 GLN cc_start: 0.7172 (mp10) cc_final: 0.6832 (tp40) REVERT: B 590 TYR cc_start: 0.8770 (t80) cc_final: 0.7663 (t80) REVERT: B 867 SER cc_start: 0.8122 (m) cc_final: 0.7551 (t) REVERT: B 956 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6887 (mm-30) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.1452 time to fit residues: 16.8212 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 266 TRP Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 975 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 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 = 0.3569 r_free = 0.3569 target = 0.133155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107566 restraints weight = 7777.748| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.09 r_work: 0.3098 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6030 Z= 0.165 Angle : 0.511 11.159 8177 Z= 0.260 Chirality : 0.040 0.138 938 Planarity : 0.003 0.034 1033 Dihedral : 10.951 171.802 907 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.13 % Favored : 91.73 % Rotamer: Outliers : 1.80 % Allowed : 15.71 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.31 (0.32), residues: 738 helix: 1.04 (0.29), residues: 365 sheet: 1.49 (0.64), residues: 70 loop : -2.31 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 295 HIS 0.002 0.001 HIS B 443 PHE 0.010 0.001 PHE B 424 TYR 0.020 0.001 TYR B 203 ARG 0.003 0.000 ARG B 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.96 seconds wall clock time: 52 minutes 7.42 seconds (3127.42 seconds total)