Starting phenix.real_space_refine on Tue Mar 3 14:26:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z52_14513/03_2026/7z52_14513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z52_14513/03_2026/7z52_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z52_14513/03_2026/7z52_14513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z52_14513/03_2026/7z52_14513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z52_14513/03_2026/7z52_14513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z52_14513/03_2026/7z52_14513.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 4, 'GLU:plan': 8, 'TYR:plan': 1, '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: {'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 1.10, per 1000 atoms: 0.19 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: 0.52 Conformation dependent library (CDL) restraints added in 218.0 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: 0.21 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: 0.86 Time building geometry restraints manager: 0.69 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: 1.590 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.260 ------------------------------------------------------------------------------- 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= 0.204 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (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 ARG 0.005 0.000 ARG B 502 TYR 0.011 0.001 TYR B 590 PHE 0.015 0.002 PHE B 563 TRP 0.015 0.001 TRP B 266 HIS 0.003 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6030) covalent geometry : angle 0.66041 ( 8177) hydrogen bonds : bond 0.17008 ( 245) hydrogen bonds : angle 5.36687 ( 705) *********************** 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 : 0.220 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: 0.8216 (ttm) cc_final: 0.7884 (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: 0.7079 (p0) cc_final: 0.6339 (p0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0869 time to fit residues: 13.6192 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.133793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107199 restraints weight = 7481.041| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.11 r_work: 0.3087 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6030 Z= 0.180 Angle : 0.609 10.160 8177 Z= 0.314 Chirality : 0.044 0.167 938 Planarity : 0.004 0.037 1033 Dihedral : 11.646 172.594 907 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.67 % Favored : 91.19 % Rotamer: Outliers : 1.64 % Allowed : 7.86 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.30), residues: 738 helix: -0.08 (0.28), residues: 369 sheet: 0.38 (0.61), residues: 83 loop : -2.36 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 262 TYR 0.012 0.001 TYR B 319 PHE 0.013 0.002 PHE B 563 TRP 0.005 0.001 TRP B 266 HIS 0.003 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 6030) covalent geometry : angle 0.60902 ( 8177) hydrogen bonds : bond 0.04671 ( 245) hydrogen bonds : angle 4.24170 ( 705) *********************** 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 81 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 120 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7234 (tm-30) REVERT: B 203 TYR cc_start: 0.8890 (t80) cc_final: 0.8673 (t80) REVERT: B 440 GLN cc_start: 0.7239 (mp10) cc_final: 0.6769 (tp40) REVERT: B 569 MET cc_start: 0.8675 (ttm) cc_final: 0.8439 (ttm) REVERT: B 590 TYR cc_start: 0.8768 (t80) cc_final: 0.7713 (t80) REVERT: B 596 ARG cc_start: 0.6767 (mmm160) cc_final: 0.6285 (mmm160) REVERT: B 872 MET cc_start: 0.8256 (tpp) cc_final: 0.7919 (tpp) REVERT: B 1042 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8219 (mp) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.0727 time to fit residues: 7.5035 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 216 VAL Chi-restraints excluded: chain B residue 341 ASP 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 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 58 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.129767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103934 restraints weight = 7618.028| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.06 r_work: 0.3048 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6030 Z= 0.181 Angle : 0.592 9.924 8177 Z= 0.306 Chirality : 0.044 0.150 938 Planarity : 0.004 0.034 1033 Dihedral : 11.613 172.430 907 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 2.29 % Allowed : 10.31 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.30), residues: 738 helix: 0.07 (0.27), residues: 371 sheet: 0.35 (0.61), residues: 83 loop : -2.32 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 502 TYR 0.013 0.001 TYR B 319 PHE 0.015 0.002 PHE B 563 TRP 0.004 0.001 TRP B 266 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 6030) covalent geometry : angle 0.59235 ( 8177) hydrogen bonds : bond 0.04473 ( 245) hydrogen bonds : angle 4.05635 ( 705) *********************** 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 83 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.205 Fit side-chains REVERT: B 120 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7260 (tm-30) REVERT: B 440 GLN cc_start: 0.7236 (mp10) cc_final: 0.6826 (tp40) REVERT: B 590 TYR cc_start: 0.8881 (t80) cc_final: 0.7835 (t80) REVERT: B 872 MET cc_start: 0.8291 (tpp) cc_final: 0.8010 (tpp) REVERT: B 1042 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8315 (mp) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 0.0666 time to fit residues: 7.2417 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 : 0.229 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 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 = 0.3512 r_free = 0.3512 target = 0.128637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102776 restraints weight = 7712.905| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.06 r_work: 0.3036 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6030 Z= 0.186 Angle : 0.592 10.053 8177 Z= 0.304 Chirality : 0.044 0.144 938 Planarity : 0.004 0.032 1033 Dihedral : 11.574 171.640 907 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 2.95 % Allowed : 12.77 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.31), residues: 738 helix: 0.22 (0.28), residues: 369 sheet: 0.20 (0.61), residues: 83 loop : -2.28 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 687 TYR 0.017 0.001 TYR B 203 PHE 0.014 0.002 PHE B 563 TRP 0.005 0.001 TRP B 266 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6030) covalent geometry : angle 0.59151 ( 8177) hydrogen bonds : bond 0.04446 ( 245) hydrogen bonds : angle 3.99941 ( 705) *********************** 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 81 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.230 Fit side-chains REVERT: B 120 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7282 (tm-30) REVERT: B 440 GLN cc_start: 0.7305 (mp10) cc_final: 0.6893 (tp40) REVERT: B 590 TYR cc_start: 0.8868 (t80) cc_final: 0.7799 (t80) REVERT: B 867 SER cc_start: 0.8216 (m) cc_final: 0.7657 (t) REVERT: B 872 MET cc_start: 0.8270 (tpp) cc_final: 0.8015 (tpp) outliers start: 18 outliers final: 13 residues processed: 74 average time/residue: 0.0617 time to fit residues: 6.5562 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 : 0.206 ------------------------------------------------------------------------------- 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 569 MET Chi-restraints excluded: chain B residue 975 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.132065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106131 restraints weight = 7701.972| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.08 r_work: 0.3085 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2779 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= 0.116 Angle : 0.526 8.880 8177 Z= 0.271 Chirality : 0.041 0.140 938 Planarity : 0.003 0.034 1033 Dihedral : 11.385 172.438 907 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 2.95 % Allowed : 13.42 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.31), residues: 738 helix: 0.52 (0.28), residues: 370 sheet: 0.31 (0.61), residues: 83 loop : -2.21 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 502 TYR 0.007 0.001 TYR B 319 PHE 0.009 0.001 PHE B 281 TRP 0.007 0.001 TRP B 295 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6030) covalent geometry : angle 0.52602 ( 8177) hydrogen bonds : bond 0.03445 ( 245) hydrogen bonds : angle 3.67469 ( 705) *********************** 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 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.222 Fit side-chains REVERT: B 120 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7181 (tm-30) REVERT: B 440 GLN cc_start: 0.7233 (mp10) cc_final: 0.6840 (tp40) REVERT: B 590 TYR cc_start: 0.8866 (t80) cc_final: 0.7828 (t80) REVERT: B 867 SER cc_start: 0.8182 (m) cc_final: 0.7620 (t) outliers start: 18 outliers final: 8 residues processed: 78 average time/residue: 0.0644 time to fit residues: 7.2168 Evaluate side-chains 72 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0770 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.130463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104690 restraints weight = 7672.758| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.07 r_work: 0.3060 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6030 Z= 0.136 Angle : 0.537 9.656 8177 Z= 0.276 Chirality : 0.042 0.137 938 Planarity : 0.003 0.033 1033 Dihedral : 11.287 167.816 907 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 2.95 % Allowed : 14.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.31), residues: 738 helix: 0.69 (0.28), residues: 364 sheet: 0.34 (0.62), residues: 83 loop : -2.27 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 510 TYR 0.009 0.001 TYR B 319 PHE 0.012 0.001 PHE B 504 TRP 0.004 0.001 TRP B 295 HIS 0.004 0.001 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6030) covalent geometry : angle 0.53715 ( 8177) hydrogen bonds : bond 0.03755 ( 245) hydrogen bonds : angle 3.68566 ( 705) *********************** 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 84 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.233 Fit side-chains REVERT: B 440 GLN cc_start: 0.7274 (mp10) cc_final: 0.6910 (tp40) REVERT: B 590 TYR cc_start: 0.8865 (t80) cc_final: 0.7796 (t80) REVERT: B 867 SER cc_start: 0.8200 (m) cc_final: 0.7635 (t) outliers start: 18 outliers final: 13 residues processed: 77 average time/residue: 0.0536 time to fit residues: 6.1720 Evaluate side-chains 76 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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 885 GLU 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 57 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.131753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105900 restraints weight = 7712.876| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.09 r_work: 0.3078 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6030 Z= 0.116 Angle : 0.514 9.170 8177 Z= 0.264 Chirality : 0.041 0.135 938 Planarity : 0.003 0.034 1033 Dihedral : 11.220 169.437 907 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.28 % Rotamer: Outliers : 3.44 % Allowed : 14.40 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.32), residues: 738 helix: 0.81 (0.29), residues: 365 sheet: 0.56 (0.62), residues: 81 loop : -2.26 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 502 TYR 0.007 0.001 TYR B 199 PHE 0.012 0.001 PHE B 504 TRP 0.005 0.001 TRP B 295 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6030) covalent geometry : angle 0.51391 ( 8177) hydrogen bonds : bond 0.03361 ( 245) hydrogen bonds : angle 3.53967 ( 705) *********************** 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 84 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.232 Fit side-chains REVERT: B 440 GLN cc_start: 0.7221 (mp10) cc_final: 0.6865 (tp40) REVERT: B 590 TYR cc_start: 0.8848 (t80) cc_final: 0.7784 (t80) REVERT: B 867 SER cc_start: 0.8192 (m) cc_final: 0.7618 (t) outliers start: 21 outliers final: 13 residues processed: 76 average time/residue: 0.0537 time to fit residues: 6.0749 Evaluate side-chains 75 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 4 optimal weight: 0.0980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.132634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107111 restraints weight = 7582.780| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.06 r_work: 0.3098 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6030 Z= 0.105 Angle : 0.506 9.648 8177 Z= 0.259 Chirality : 0.040 0.134 938 Planarity : 0.003 0.034 1033 Dihedral : 11.153 171.004 907 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.32 % Favored : 92.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.32), residues: 738 helix: 0.93 (0.29), residues: 365 sheet: 0.59 (0.62), residues: 81 loop : -2.25 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 502 TYR 0.020 0.001 TYR B 203 PHE 0.011 0.001 PHE B 504 TRP 0.006 0.001 TRP B 295 HIS 0.003 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6030) covalent geometry : angle 0.50552 ( 8177) hydrogen bonds : bond 0.03162 ( 245) hydrogen bonds : angle 3.46362 ( 705) *********************** 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 80 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.221 Fit side-chains REVERT: B 385 ASN cc_start: 0.8421 (m-40) cc_final: 0.7927 (t0) REVERT: B 440 GLN cc_start: 0.7194 (mp10) cc_final: 0.6843 (tp40) REVERT: B 590 TYR cc_start: 0.8826 (t80) cc_final: 0.7773 (t80) REVERT: B 867 SER cc_start: 0.8150 (m) cc_final: 0.7571 (t) outliers start: 13 outliers final: 12 residues processed: 75 average time/residue: 0.0517 time to fit residues: 5.7544 Evaluate side-chains 75 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.127231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101488 restraints weight = 7807.835| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.10 r_work: 0.3072 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6030 Z= 0.114 Angle : 0.517 10.316 8177 Z= 0.264 Chirality : 0.040 0.136 938 Planarity : 0.003 0.034 1033 Dihedral : 11.140 171.406 907 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.45 % Favored : 92.41 % Rotamer: Outliers : 2.29 % Allowed : 15.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.32), residues: 738 helix: 0.97 (0.29), residues: 365 sheet: 0.61 (0.62), residues: 81 loop : -2.23 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 502 TYR 0.008 0.001 TYR B 319 PHE 0.010 0.001 PHE B 504 TRP 0.005 0.001 TRP B 295 HIS 0.003 0.001 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6030) covalent geometry : angle 0.51703 ( 8177) hydrogen bonds : bond 0.03313 ( 245) hydrogen bonds : angle 3.47259 ( 705) *********************** 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 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.214 Fit side-chains REVERT: B 440 GLN cc_start: 0.7214 (mp10) cc_final: 0.6864 (tp40) REVERT: B 559 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8454 (tp) REVERT: B 590 TYR cc_start: 0.8849 (t80) cc_final: 0.7781 (t80) REVERT: B 867 SER cc_start: 0.8175 (m) cc_final: 0.7599 (t) REVERT: B 956 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6829 (mm-30) outliers start: 14 outliers final: 12 residues processed: 72 average time/residue: 0.0486 time to fit residues: 5.2460 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 : 0.203 ------------------------------------------------------------------------------- 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 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.0030 chunk 32 optimal weight: 0.4980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 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 = 0.3522 r_free = 0.3522 target = 0.129287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104033 restraints weight = 7745.543| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.06 r_work: 0.3041 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6030 Z= 0.146 Angle : 0.550 11.167 8177 Z= 0.281 Chirality : 0.042 0.137 938 Planarity : 0.003 0.033 1033 Dihedral : 11.153 170.298 907 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.99 % Favored : 91.87 % Rotamer: Outliers : 2.95 % Allowed : 14.89 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.32), residues: 738 helix: 0.86 (0.28), residues: 365 sheet: 0.52 (0.63), residues: 81 loop : -2.23 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 510 TYR 0.020 0.001 TYR B 203 PHE 0.011 0.001 PHE B 563 TRP 0.004 0.001 TRP B 266 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6030) covalent geometry : angle 0.54969 ( 8177) hydrogen bonds : bond 0.03810 ( 245) hydrogen bonds : angle 3.62110 ( 705) ********************** 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 80 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.186 Fit side-chains REVERT: B 266 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.6438 (t-100) REVERT: B 385 ASN cc_start: 0.8478 (m-40) cc_final: 0.7980 (t0) REVERT: B 440 GLN cc_start: 0.7286 (mp10) cc_final: 0.6925 (tp40) REVERT: B 590 TYR cc_start: 0.8873 (t80) cc_final: 0.7788 (t80) REVERT: B 867 SER cc_start: 0.8227 (m) cc_final: 0.7661 (t) REVERT: B 956 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6875 (mm-30) outliers start: 18 outliers final: 13 residues processed: 74 average time/residue: 0.0546 time to fit residues: 5.9962 Evaluate side-chains 76 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.130665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105540 restraints weight = 7668.790| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.05 r_work: 0.3072 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3156 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= 0.122 Angle : 0.528 10.916 8177 Z= 0.270 Chirality : 0.041 0.135 938 Planarity : 0.003 0.033 1033 Dihedral : 11.061 170.111 907 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.28 % Rotamer: Outliers : 2.45 % Allowed : 15.88 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.32), residues: 738 helix: 0.92 (0.28), residues: 365 sheet: 0.55 (0.63), residues: 81 loop : -2.21 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 510 TYR 0.007 0.001 TYR B 319 PHE 0.010 0.001 PHE B 504 TRP 0.004 0.001 TRP B 295 HIS 0.003 0.001 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6030) covalent geometry : angle 0.52796 ( 8177) hydrogen bonds : bond 0.03453 ( 245) hydrogen bonds : angle 3.56518 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1400.86 seconds wall clock time: 24 minutes 38.90 seconds (1478.90 seconds total)