Starting phenix.real_space_refine on Tue Mar 11 14:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z52_14513/03_2025/7z52_14513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z52_14513/03_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_14513/03_2025/7z52_14513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z52_14513/03_2025/7z52_14513.map" model { file = "/net/cci-nas-00/data/ceres_data/7z52_14513/03_2025/7z52_14513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z52_14513/03_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-5624/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: 4.76, per 1000 atoms: 0.81 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: 2.21 Conformation dependent library (CDL) restraints added in 975.5 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: 0.69 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: 1.73 Time building geometry restraints manager: 1.96 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.970 Find NCS groups from input model: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- 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 : 0.664 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: 0.2096 time to fit residues: 32.7820 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 : 0.668 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109329 restraints weight = 7319.868| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.10 r_work: 0.3119 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- 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 : 0.611 Fit side-chains revert: symmetry clash REVERT: B 120 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7189 (tm-30) REVERT: B 203 TYR cc_start: 0.8863 (t80) cc_final: 0.8652 (t80) REVERT: B 440 GLN cc_start: 0.7117 (mp10) cc_final: 0.6651 (tp40) REVERT: B 569 MET cc_start: 0.8648 (ttm) cc_final: 0.8431 (ttm) REVERT: B 590 TYR cc_start: 0.8702 (t80) cc_final: 0.7640 (t80) REVERT: B 872 MET cc_start: 0.8137 (tpp) cc_final: 0.7851 (tpp) REVERT: B 1042 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8161 (mp) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.1707 time to fit residues: 18.1653 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 : 0.604 ------------------------------------------------------------------------------- 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: 0.7980 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.135863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109491 restraints weight = 7454.065| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.08 r_work: 0.3117 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2153 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= 0.190 Angle : 0.527 9.185 8177 Z= 0.271 Chirality : 0.041 0.145 938 Planarity : 0.003 0.033 1033 Dihedral : 11.379 174.138 907 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.32 % Favored : 92.55 % Rotamer: Outliers : 1.96 % Allowed : 10.15 % Favored : 87.89 % 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: -0.91 (0.31), residues: 738 helix: 0.44 (0.28), residues: 364 sheet: 0.56 (0.62), residues: 83 loop : -2.37 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 266 HIS 0.003 0.001 HIS B 300 PHE 0.010 0.001 PHE B 424 TYR 0.009 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 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.651 Fit side-chains REVERT: B 440 GLN cc_start: 0.7134 (mp10) cc_final: 0.6702 (tp40) REVERT: B 559 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8393 (tp) REVERT: B 590 TYR cc_start: 0.8734 (t80) cc_final: 0.7683 (t80) REVERT: B 872 MET cc_start: 0.8142 (tpp) cc_final: 0.7858 (tpp) REVERT: B 1042 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8145 (mp) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.1685 time to fit residues: 17.8835 Evaluate side-chains 75 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 380 MET Chi-restraints excluded: chain B residue 429 ASP 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: 0.0010 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 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: 0.2980 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.133511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107937 restraints weight = 7681.909| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.04 r_work: 0.3120 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2411 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= 0.182 Angle : 0.514 8.941 8177 Z= 0.263 Chirality : 0.041 0.142 938 Planarity : 0.003 0.033 1033 Dihedral : 11.247 174.053 907 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 2.62 % Allowed : 10.47 % Favored : 86.91 % 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: -0.70 (0.31), residues: 738 helix: 0.70 (0.28), residues: 365 sheet: 0.60 (0.62), residues: 83 loop : -2.37 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 266 HIS 0.003 0.001 HIS B 300 PHE 0.010 0.001 PHE B 424 TYR 0.008 0.001 TYR B 319 ARG 0.002 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 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.611 Fit side-chains REVERT: B 440 GLN cc_start: 0.7109 (mp10) cc_final: 0.6727 (tp40) REVERT: B 590 TYR cc_start: 0.8802 (t80) cc_final: 0.7741 (t80) REVERT: B 1042 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8137 (mp) outliers start: 16 outliers final: 9 residues processed: 78 average time/residue: 0.1634 time to fit residues: 17.7570 Evaluate side-chains 75 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 1042 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.0030 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.4370 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.136055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110169 restraints weight = 7565.380| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.05 r_work: 0.3136 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6030 Z= 0.152 Angle : 0.496 9.056 8177 Z= 0.254 Chirality : 0.040 0.135 938 Planarity : 0.003 0.034 1033 Dihedral : 11.066 174.482 907 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 1.96 % Allowed : 12.11 % Favored : 85.92 % 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: -0.44 (0.31), residues: 738 helix: 0.98 (0.29), residues: 358 sheet: 0.76 (0.62), residues: 82 loop : -2.27 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 511 HIS 0.002 0.001 HIS B 300 PHE 0.010 0.001 PHE B 424 TYR 0.006 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 81 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.604 Fit side-chains REVERT: B 440 GLN cc_start: 0.7036 (mp10) cc_final: 0.6671 (tp40) REVERT: B 559 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8374 (tp) REVERT: B 590 TYR cc_start: 0.8767 (t80) cc_final: 0.7660 (t80) outliers start: 12 outliers final: 7 residues processed: 75 average time/residue: 0.1423 time to fit residues: 15.1529 Evaluate side-chains 75 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 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 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 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: 0.6980 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 0.0060 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.132110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106200 restraints weight = 7528.300| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.05 r_work: 0.3084 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6030 Z= 0.216 Angle : 0.520 9.803 8177 Z= 0.268 Chirality : 0.041 0.140 938 Planarity : 0.003 0.034 1033 Dihedral : 11.083 174.040 907 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % 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 : 0.14 % 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: -0.51 (0.31), residues: 738 helix: 0.86 (0.28), residues: 365 sheet: 0.71 (0.62), residues: 82 loop : -2.29 (0.32), 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 563 TYR 0.020 0.001 TYR B 203 ARG 0.002 0.000 ARG B 510 *********************** 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 : 0.598 Fit side-chains REVERT: B 440 GLN cc_start: 0.7173 (mp10) cc_final: 0.6781 (tp40) REVERT: B 590 TYR cc_start: 0.8849 (t80) cc_final: 0.7758 (t80) REVERT: B 867 SER cc_start: 0.8203 (m) cc_final: 0.7603 (t) outliers start: 18 outliers final: 13 residues processed: 76 average time/residue: 0.1368 time to fit residues: 14.9872 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 : 0.660 ------------------------------------------------------------------------------- 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 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 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 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 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: 1.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.127894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102221 restraints weight = 7660.694| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.04 r_work: 0.3027 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6030 Z= 0.324 Angle : 0.589 10.562 8177 Z= 0.305 Chirality : 0.044 0.140 938 Planarity : 0.004 0.034 1033 Dihedral : 11.229 164.648 907 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 3.27 % Allowed : 12.44 % 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 (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: -0.77 (0.31), residues: 738 helix: 0.63 (0.28), residues: 365 sheet: 0.35 (0.62), residues: 83 loop : -2.31 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 266 HIS 0.005 0.001 HIS B 300 PHE 0.017 0.002 PHE B 563 TYR 0.013 0.001 TYR B 319 ARG 0.003 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 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.675 Fit side-chains REVERT: B 440 GLN cc_start: 0.7345 (mp10) cc_final: 0.6946 (tp40) REVERT: B 590 TYR cc_start: 0.8892 (t80) cc_final: 0.7760 (t80) REVERT: B 867 SER cc_start: 0.8303 (m) cc_final: 0.7773 (t) outliers start: 20 outliers final: 15 residues processed: 79 average time/residue: 0.1351 time to fit residues: 15.6230 Evaluate side-chains 78 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 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 885 GLU 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: 3.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.132024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106320 restraints weight = 7599.405| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.07 r_work: 0.3084 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3037 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= 0.177 Angle : 0.518 10.060 8177 Z= 0.266 Chirality : 0.041 0.134 938 Planarity : 0.003 0.035 1033 Dihedral : 11.014 167.417 907 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.99 % Favored : 91.87 % Rotamer: Outliers : 2.29 % Allowed : 13.58 % 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: -0.51 (0.31), residues: 738 helix: 0.88 (0.28), residues: 365 sheet: 0.62 (0.62), residues: 81 loop : -2.27 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 511 HIS 0.003 0.001 HIS B 255 PHE 0.011 0.001 PHE B 504 TYR 0.007 0.001 TYR B 199 ARG 0.002 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 79 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.686 Fit side-chains REVERT: B 385 ASN cc_start: 0.8388 (m-40) cc_final: 0.7894 (t0) REVERT: B 440 GLN cc_start: 0.7228 (mp10) cc_final: 0.6866 (tp40) REVERT: B 590 TYR cc_start: 0.8828 (t80) cc_final: 0.7745 (t80) REVERT: B 867 SER cc_start: 0.8210 (m) cc_final: 0.7652 (t) REVERT: B 956 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6880 (mm-30) outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.1399 time to fit residues: 15.0182 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 : 0.685 ------------------------------------------------------------------------------- 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 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 885 GLU 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: 0.4980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.131365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105900 restraints weight = 7618.578| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.06 r_work: 0.3067 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3082 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= 0.198 Angle : 0.527 10.590 8177 Z= 0.270 Chirality : 0.041 0.136 938 Planarity : 0.003 0.034 1033 Dihedral : 10.925 169.693 907 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 2.13 % Allowed : 14.73 % Favored : 83.14 % 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: -0.47 (0.31), residues: 738 helix: 0.91 (0.29), residues: 365 sheet: 0.60 (0.62), residues: 81 loop : -2.25 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 295 HIS 0.004 0.001 HIS B 300 PHE 0.012 0.001 PHE B1036 TYR 0.020 0.001 TYR B 203 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 74 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.687 Fit side-chains REVERT: B 440 GLN cc_start: 0.7223 (mp10) cc_final: 0.6855 (tp40) REVERT: B 590 TYR cc_start: 0.8829 (t80) cc_final: 0.7757 (t80) REVERT: B 867 SER cc_start: 0.8195 (m) cc_final: 0.7628 (t) REVERT: B 956 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6902 (mm-30) outliers start: 13 outliers final: 13 residues processed: 68 average time/residue: 0.1382 time to fit residues: 13.7552 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 : 0.601 ------------------------------------------------------------------------------- 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 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 885 GLU 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 19 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106875 restraints weight = 7638.629| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.05 r_work: 0.3091 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3140 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= 0.188 Angle : 0.519 10.239 8177 Z= 0.266 Chirality : 0.040 0.137 938 Planarity : 0.003 0.034 1033 Dihedral : 10.850 170.364 907 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 2.29 % Allowed : 14.57 % Favored : 83.14 % 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: -0.41 (0.32), residues: 738 helix: 0.96 (0.29), residues: 365 sheet: 0.60 (0.62), residues: 81 loop : -2.20 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 295 HIS 0.003 0.001 HIS B 300 PHE 0.010 0.001 PHE B1036 TYR 0.007 0.001 TYR B 319 ARG 0.002 0.000 ARG B 510 ********************** 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: 14 poor density : 66 time to evaluate : 0.662 Fit side-chains REVERT: B 385 ASN cc_start: 0.8385 (m-40) cc_final: 0.7883 (t0) REVERT: B 440 GLN cc_start: 0.7209 (mp10) cc_final: 0.6853 (tp40) REVERT: B 590 TYR cc_start: 0.8811 (t80) cc_final: 0.7751 (t80) REVERT: B 867 SER cc_start: 0.8154 (m) cc_final: 0.7584 (t) REVERT: B 956 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6903 (mm-30) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.1437 time to fit residues: 15.3090 Evaluate side-chains 76 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 885 GLU 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 47 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.0270 chunk 51 optimal weight: 0.2980 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106610 restraints weight = 7746.992| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.06 r_work: 0.3100 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3175 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= 0.167 Angle : 0.507 10.759 8177 Z= 0.259 Chirality : 0.040 0.136 938 Planarity : 0.003 0.034 1033 Dihedral : 10.754 171.018 907 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 2.13 % Allowed : 14.40 % Favored : 83.47 % 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: -0.35 (0.32), residues: 738 helix: 1.01 (0.29), residues: 365 sheet: 0.63 (0.62), residues: 81 loop : -2.17 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 295 HIS 0.002 0.001 HIS B 300 PHE 0.013 0.001 PHE B1036 TYR 0.019 0.001 TYR B 203 ARG 0.002 0.000 ARG B 510 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.10 seconds wall clock time: 49 minutes 4.81 seconds (2944.81 seconds total)