Starting phenix.real_space_refine on Wed Feb 4 01:55:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qig_53187/02_2026/9qig_53187_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qig_53187/02_2026/9qig_53187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qig_53187/02_2026/9qig_53187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qig_53187/02_2026/9qig_53187.map" model { file = "/net/cci-nas-00/data/ceres_data/9qig_53187/02_2026/9qig_53187_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qig_53187/02_2026/9qig_53187_neut.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.025 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 9 5.49 5 S 37 5.16 5 C 5139 2.51 5 N 1348 2.21 5 O 1544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8077 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8010 Classifications: {'peptide': 1011} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 50, 'TRANS': 955} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ATP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.17, per 1000 atoms: 0.27 Number of scatterers: 8077 At special positions: 0 Unit cell: (81.675, 103.95, 121.275, 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 37 16.00 P 9 15.00 O 1544 8.00 N 1348 7.00 C 5139 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: 0.73 Conformation dependent library (CDL) restraints added in 300.7 milliseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 48.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 40 through 52 removed outlier: 7.422A pdb=" N ARG B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.546A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N HIS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.556A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 301 through 308 removed outlier: 4.376A pdb=" N LYS B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.722A pdb=" N THR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 387 through 408 Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.071A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 443 through 451 Processing helix chain 'B' and resid 451 through 460 Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'B' and resid 546 through 552 removed outlier: 4.192A pdb=" N THR B 551 " --> pdb=" O THR B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 585 removed outlier: 3.666A pdb=" N ARG B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 633 through 650 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 779 through 790 removed outlier: 3.994A pdb=" N GLU B 789 " --> pdb=" O ASN B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 834 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 894 through 914 Processing helix chain 'B' and resid 917 through 920 Processing helix chain 'B' and resid 967 through 979 Processing helix chain 'B' and resid 1001 through 1007 removed outlier: 3.728A pdb=" N LEU B1005 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1014 Processing sheet with id=AA1, first strand: chain 'B' and resid 134 through 138 removed outlier: 3.878A pdb=" N CYS B 156 " --> pdb=" O HIS B 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA3, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.998A pdb=" N GLY B 274 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 229 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N SER B 272 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS B 231 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER B 270 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER B 272 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL B 265 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.477A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE B 463 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR B 496 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 465 " --> pdb=" O THR B 496 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 563 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 564 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N SER B 591 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 566 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR B 593 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL B 602 " --> pdb=" O LYS B 922 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LYS B 922 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 944 through 947 removed outlier: 6.659A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.572A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B1027 " --> pdb=" O MET B 985 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET B 985 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 986 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.572A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1092 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: 1.43 Time building geometry restraints manager: 0.96 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: 2611 1.34 - 1.46: 1775 1.46 - 1.58: 3815 1.58 - 1.69: 8 1.69 - 1.81: 53 Bond restraints: 8262 Sorted by residual: bond pdb=" CA HIS B 515 " pdb=" C HIS B 515 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.41e-02 5.03e+03 2.01e+00 bond pdb=" CB ILE B 638 " pdb=" CG2 ILE B 638 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CB LYS B 658 " pdb=" CG LYS B 658 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" C GLN B 518 " pdb=" N LYS B 519 " ideal model delta sigma weight residual 1.327 1.306 0.021 1.71e-02 3.42e+03 1.45e+00 bond pdb=" CA ASN B 234 " pdb=" CB ASN B 234 " ideal model delta sigma weight residual 1.533 1.552 -0.018 1.66e-02 3.63e+03 1.19e+00 ... (remaining 8257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 11052 2.28 - 4.57: 153 4.57 - 6.85: 11 6.85 - 9.13: 3 9.13 - 11.42: 3 Bond angle restraints: 11222 Sorted by residual: angle pdb=" CA LYS B 658 " pdb=" CB LYS B 658 " pdb=" CG LYS B 658 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CB MET B 985 " pdb=" CG MET B 985 " pdb=" SD MET B 985 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" N PHE B 106 " pdb=" CA PHE B 106 " pdb=" C PHE B 106 " ideal model delta sigma weight residual 114.56 109.92 4.64 1.27e+00 6.20e-01 1.34e+01 angle pdb=" CB MET B 162 " pdb=" CG MET B 162 " pdb=" SD MET B 162 " ideal model delta sigma weight residual 112.70 122.50 -9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C PRO B 514 " pdb=" N HIS B 515 " pdb=" CA HIS B 515 " ideal model delta sigma weight residual 121.94 115.70 6.24 2.00e+00 2.50e-01 9.73e+00 ... (remaining 11217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4605 17.87 - 35.73: 347 35.73 - 53.59: 62 53.59 - 71.46: 20 71.46 - 89.32: 10 Dihedral angle restraints: 5044 sinusoidal: 2087 harmonic: 2957 Sorted by residual: dihedral pdb=" CA MET B 992 " pdb=" C MET B 992 " pdb=" N LEU B 993 " pdb=" CA LEU B 993 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASN B 251 " pdb=" C ASN B 251 " pdb=" N GLY B 252 " pdb=" CA GLY B 252 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR B 44 " pdb=" C TYR B 44 " pdb=" N SER B 45 " pdb=" CA SER B 45 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 881 0.034 - 0.068: 252 0.068 - 0.102: 96 0.102 - 0.136: 37 0.136 - 0.170: 2 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA ASN B 234 " pdb=" N ASN B 234 " pdb=" C ASN B 234 " pdb=" CB ASN B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA VAL B 995 " pdb=" N VAL B 995 " pdb=" C VAL B 995 " pdb=" CB VAL B 995 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CG LEU B 403 " pdb=" CB LEU B 403 " pdb=" CD1 LEU B 403 " pdb=" CD2 LEU B 403 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1265 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 995 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO B 996 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 996 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 996 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 267 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO B 268 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 658 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C LYS B 658 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS B 658 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE B 659 " 0.008 2.00e-02 2.50e+03 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4720 2.99 - 3.47: 9215 3.47 - 3.95: 13913 3.95 - 4.42: 16508 4.42 - 4.90: 24294 Nonbonded interactions: 68650 Sorted by model distance: nonbonded pdb=" O TRP B 640 " pdb=" OD1 ASP B 643 " model vdw 2.514 3.040 nonbonded pdb=" O GLU B 233 " pdb=" OD1 ASN B 234 " model vdw 2.564 3.040 nonbonded pdb=" O2' ATP B1102 " pdb=" O3' ATP B1102 " model vdw 2.600 2.432 nonbonded pdb=" O GLN B 639 " pdb=" OD1 ASP B 643 " model vdw 2.601 3.040 nonbonded pdb=" N SER B 267 " pdb=" O SER B 267 " model vdw 2.602 2.496 ... (remaining 68645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 0.041 8262 Z= 0.218 Angle : 0.685 11.415 11222 Z= 0.380 Chirality : 0.040 0.170 1268 Planarity : 0.004 0.039 1430 Dihedral : 13.796 89.324 3122 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.45 % Allowed : 8.51 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.11 (0.27), residues: 1009 helix: 1.81 (0.26), residues: 422 sheet: -0.35 (0.42), residues: 150 loop : 0.20 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 48 TYR 0.014 0.002 TYR B1021 PHE 0.018 0.002 PHE B 683 TRP 0.012 0.001 TRP B 660 HIS 0.006 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8262) covalent geometry : angle 0.68550 (11222) hydrogen bonds : bond 0.15498 ( 394) hydrogen bonds : angle 6.96174 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.9309 (ptp) cc_final: 0.8907 (mpp) REVERT: B 400 GLN cc_start: 0.9457 (tm-30) cc_final: 0.9098 (tm-30) REVERT: B 475 MET cc_start: 0.9599 (mmm) cc_final: 0.9268 (mmm) REVERT: B 649 PHE cc_start: 0.9435 (m-80) cc_final: 0.8948 (m-80) REVERT: B 844 MET cc_start: 0.8837 (ptp) cc_final: 0.8436 (mtm) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.0732 time to fit residues: 4.1292 Evaluate side-chains 34 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 683 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 599 HIS ** B 713 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 = 0.2788 r_free = 0.2788 target = 0.029065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.022444 restraints weight = 84586.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.023189 restraints weight = 54803.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.023715 restraints weight = 40515.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.024080 restraints weight = 32398.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.024451 restraints weight = 27333.651| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8262 Z= 0.150 Angle : 0.561 7.715 11222 Z= 0.294 Chirality : 0.041 0.171 1268 Planarity : 0.004 0.036 1430 Dihedral : 7.190 69.961 1155 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.34 % Allowed : 8.29 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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 (0.28), residues: 1009 helix: 1.81 (0.26), residues: 440 sheet: -0.25 (0.43), residues: 150 loop : 0.03 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 248 TYR 0.011 0.001 TYR B 663 PHE 0.011 0.001 PHE B1028 TRP 0.012 0.001 TRP B 660 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8262) covalent geometry : angle 0.56092 (11222) hydrogen bonds : bond 0.04135 ( 394) hydrogen bonds : angle 5.43408 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.9302 (mmt) cc_final: 0.9064 (mmp) REVERT: B 400 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9226 (tm-30) REVERT: B 403 LEU cc_start: 0.9842 (OUTLIER) cc_final: 0.9618 (mt) REVERT: B 475 MET cc_start: 0.9590 (mmm) cc_final: 0.9288 (mmm) REVERT: B 649 PHE cc_start: 0.9423 (m-80) cc_final: 0.8658 (m-80) REVERT: B 844 MET cc_start: 0.8830 (ptp) cc_final: 0.8363 (mtm) outliers start: 12 outliers final: 5 residues processed: 41 average time/residue: 0.0640 time to fit residues: 4.2442 Evaluate side-chains 35 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 971 PHE Chi-restraints excluded: chain B residue 1019 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 713 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.029118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.021908 restraints weight = 83759.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.022667 restraints weight = 54812.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.023203 restraints weight = 40405.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.023630 restraints weight = 32299.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.023927 restraints weight = 27004.525| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8262 Z= 0.122 Angle : 0.528 8.518 11222 Z= 0.274 Chirality : 0.040 0.170 1268 Planarity : 0.004 0.036 1430 Dihedral : 6.899 71.253 1152 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.23 % Allowed : 8.06 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.14 (0.28), residues: 1009 helix: 1.90 (0.26), residues: 440 sheet: -0.30 (0.42), residues: 150 loop : 0.02 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 691 TYR 0.011 0.001 TYR B 663 PHE 0.011 0.001 PHE B 656 TRP 0.010 0.001 TRP B 660 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8262) covalent geometry : angle 0.52835 (11222) hydrogen bonds : bond 0.03480 ( 394) hydrogen bonds : angle 5.02965 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.9370 (mmt) cc_final: 0.9166 (mmp) REVERT: B 400 GLN cc_start: 0.9512 (tm-30) cc_final: 0.9210 (tm-30) REVERT: B 474 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9032 (mt-10) REVERT: B 475 MET cc_start: 0.9582 (mmm) cc_final: 0.9304 (mmm) REVERT: B 649 PHE cc_start: 0.9383 (m-80) cc_final: 0.8678 (m-80) REVERT: B 844 MET cc_start: 0.8858 (ptp) cc_final: 0.8259 (mtp) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.0721 time to fit residues: 4.6640 Evaluate side-chains 36 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 971 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 712 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.029406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.022798 restraints weight = 82715.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.023557 restraints weight = 53751.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.024115 restraints weight = 39602.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.024537 restraints weight = 31478.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.024856 restraints weight = 26363.923| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8262 Z= 0.110 Angle : 0.524 9.702 11222 Z= 0.268 Chirality : 0.040 0.171 1268 Planarity : 0.003 0.038 1430 Dihedral : 6.671 71.278 1150 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.90 % Allowed : 9.07 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.26 (0.28), residues: 1009 helix: 1.96 (0.26), residues: 440 sheet: -0.31 (0.43), residues: 151 loop : 0.18 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 947 TYR 0.010 0.001 TYR B 663 PHE 0.011 0.001 PHE B 656 TRP 0.009 0.001 TRP B 660 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8262) covalent geometry : angle 0.52352 (11222) hydrogen bonds : bond 0.03106 ( 394) hydrogen bonds : angle 4.84922 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.9358 (mmt) cc_final: 0.9132 (mmp) REVERT: B 400 GLN cc_start: 0.9597 (tm-30) cc_final: 0.9299 (tm-30) REVERT: B 474 GLU cc_start: 0.9574 (mm-30) cc_final: 0.8992 (mt-10) REVERT: B 475 MET cc_start: 0.9536 (mmm) cc_final: 0.9333 (mmm) REVERT: B 649 PHE cc_start: 0.9360 (m-80) cc_final: 0.8628 (m-80) REVERT: B 844 MET cc_start: 0.8794 (ptp) cc_final: 0.8187 (mtp) REVERT: B 872 MET cc_start: 0.9512 (ttt) cc_final: 0.9235 (tpp) outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.0686 time to fit residues: 4.5431 Evaluate side-chains 37 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 971 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1001 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.028740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.022198 restraints weight = 85282.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.022925 restraints weight = 55502.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.023481 restraints weight = 40990.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.023886 restraints weight = 32585.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.024130 restraints weight = 27304.849| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8262 Z= 0.187 Angle : 0.557 8.246 11222 Z= 0.289 Chirality : 0.039 0.167 1268 Planarity : 0.004 0.034 1430 Dihedral : 6.803 76.152 1150 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.57 % Allowed : 9.52 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.13 (0.28), residues: 1009 helix: 1.93 (0.26), residues: 440 sheet: -0.42 (0.41), residues: 158 loop : 0.04 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 809 TYR 0.010 0.001 TYR B 663 PHE 0.011 0.001 PHE B 649 TRP 0.009 0.001 TRP B 660 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8262) covalent geometry : angle 0.55718 (11222) hydrogen bonds : bond 0.03323 ( 394) hydrogen bonds : angle 4.92802 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.9357 (mmt) cc_final: 0.9152 (mmp) REVERT: B 400 GLN cc_start: 0.9611 (tm-30) cc_final: 0.9329 (tm-30) REVERT: B 474 GLU cc_start: 0.9586 (mm-30) cc_final: 0.8995 (mt-10) REVERT: B 649 PHE cc_start: 0.9396 (m-80) cc_final: 0.8673 (m-80) REVERT: B 844 MET cc_start: 0.8781 (ptp) cc_final: 0.8285 (mtm) REVERT: B 998 MET cc_start: 0.5762 (ppp) cc_final: 0.5482 (ppp) outliers start: 14 outliers final: 11 residues processed: 44 average time/residue: 0.0729 time to fit residues: 5.0626 Evaluate side-chains 43 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 687 LYS Chi-restraints excluded: chain B residue 971 PHE Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 997 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.2809 r_free = 0.2809 target = 0.029303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.022069 restraints weight = 82534.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.022830 restraints weight = 53812.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.023373 restraints weight = 39939.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.023752 restraints weight = 31847.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.024079 restraints weight = 26988.284| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8262 Z= 0.103 Angle : 0.513 8.782 11222 Z= 0.261 Chirality : 0.040 0.268 1268 Planarity : 0.003 0.037 1430 Dihedral : 6.718 77.531 1150 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.23 % Allowed : 10.64 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.24 (0.28), residues: 1009 helix: 2.02 (0.26), residues: 440 sheet: -0.24 (0.43), residues: 150 loop : 0.04 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 822 TYR 0.010 0.001 TYR B 663 PHE 0.021 0.001 PHE B 826 TRP 0.007 0.001 TRP B 660 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8262) covalent geometry : angle 0.51289 (11222) hydrogen bonds : bond 0.03033 ( 394) hydrogen bonds : angle 4.72815 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.9403 (mmt) cc_final: 0.9180 (mmp) REVERT: B 69 MET cc_start: 0.7586 (tpp) cc_final: 0.7369 (tpp) REVERT: B 400 GLN cc_start: 0.9598 (tm-30) cc_final: 0.9283 (tm-30) REVERT: B 475 MET cc_start: 0.9418 (mmm) cc_final: 0.9006 (mmm) REVERT: B 649 PHE cc_start: 0.9364 (m-80) cc_final: 0.8668 (m-80) REVERT: B 844 MET cc_start: 0.8824 (ptp) cc_final: 0.8492 (mtp) REVERT: B 871 LYS cc_start: 0.9652 (mmmt) cc_final: 0.9414 (mmmt) REVERT: B 872 MET cc_start: 0.9510 (ttt) cc_final: 0.9110 (tpp) outliers start: 11 outliers final: 9 residues processed: 41 average time/residue: 0.0799 time to fit residues: 5.0627 Evaluate side-chains 40 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 971 PHE Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 997 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.2803 r_free = 0.2803 target = 0.029224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.022587 restraints weight = 83944.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.023315 restraints weight = 55178.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.023854 restraints weight = 41029.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.024259 restraints weight = 32922.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.024597 restraints weight = 27718.667| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8262 Z= 0.143 Angle : 0.530 8.780 11222 Z= 0.271 Chirality : 0.039 0.206 1268 Planarity : 0.003 0.035 1430 Dihedral : 6.719 79.313 1150 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.57 % Allowed : 10.19 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.23 (0.28), residues: 1009 helix: 2.00 (0.26), residues: 440 sheet: -0.25 (0.43), residues: 150 loop : 0.03 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 809 TYR 0.010 0.001 TYR B 663 PHE 0.012 0.001 PHE B 656 TRP 0.009 0.001 TRP B 192 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8262) covalent geometry : angle 0.52980 (11222) hydrogen bonds : bond 0.03051 ( 394) hydrogen bonds : angle 4.76373 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.9413 (mmt) cc_final: 0.9074 (mmt) REVERT: B 400 GLN cc_start: 0.9625 (tm-30) cc_final: 0.9338 (tm-30) REVERT: B 475 MET cc_start: 0.9489 (mmm) cc_final: 0.9155 (mmm) REVERT: B 649 PHE cc_start: 0.9395 (m-80) cc_final: 0.8678 (m-80) REVERT: B 844 MET cc_start: 0.8785 (ptp) cc_final: 0.8152 (mtp) REVERT: B 871 LYS cc_start: 0.9661 (mmmt) cc_final: 0.9428 (mmmt) REVERT: B 872 MET cc_start: 0.9511 (ttt) cc_final: 0.9113 (tpp) outliers start: 14 outliers final: 13 residues processed: 44 average time/residue: 0.0819 time to fit residues: 5.5609 Evaluate side-chains 43 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 687 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 971 PHE Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 997 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.2804 r_free = 0.2804 target = 0.029234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.022669 restraints weight = 82825.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.023380 restraints weight = 54649.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.023949 restraints weight = 40855.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.024281 restraints weight = 32479.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.024649 restraints weight = 27705.677| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8262 Z= 0.138 Angle : 0.541 9.749 11222 Z= 0.273 Chirality : 0.039 0.167 1268 Planarity : 0.003 0.035 1430 Dihedral : 6.734 81.347 1150 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.57 % Allowed : 10.53 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.28 (0.28), residues: 1009 helix: 2.05 (0.26), residues: 440 sheet: -0.21 (0.43), residues: 150 loop : 0.05 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 809 TYR 0.011 0.001 TYR B 663 PHE 0.010 0.001 PHE B 711 TRP 0.007 0.001 TRP B 660 HIS 0.003 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8262) covalent geometry : angle 0.54131 (11222) hydrogen bonds : bond 0.03007 ( 394) hydrogen bonds : angle 4.71765 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.9416 (mmt) cc_final: 0.9078 (mmt) REVERT: B 400 GLN cc_start: 0.9625 (tm-30) cc_final: 0.9337 (tm-30) REVERT: B 475 MET cc_start: 0.9490 (mmm) cc_final: 0.9156 (mmm) REVERT: B 649 PHE cc_start: 0.9403 (m-80) cc_final: 0.8738 (m-80) REVERT: B 844 MET cc_start: 0.8792 (ptp) cc_final: 0.8143 (mtp) REVERT: B 871 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9437 (mmmt) REVERT: B 872 MET cc_start: 0.9512 (ttt) cc_final: 0.9110 (tpp) outliers start: 14 outliers final: 10 residues processed: 42 average time/residue: 0.0815 time to fit residues: 5.3018 Evaluate side-chains 40 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 971 PHE Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 997 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.2770 r_free = 0.2770 target = 0.028092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.021595 restraints weight = 85136.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.022290 restraints weight = 56222.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.022832 restraints weight = 41820.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.023209 restraints weight = 33445.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.023522 restraints weight = 28329.004| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8262 Z= 0.301 Angle : 0.682 10.123 11222 Z= 0.353 Chirality : 0.041 0.246 1268 Planarity : 0.004 0.032 1430 Dihedral : 7.167 86.828 1150 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.68 % Allowed : 10.64 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 0.89 (0.27), residues: 1009 helix: 1.61 (0.26), residues: 435 sheet: -0.35 (0.43), residues: 150 loop : -0.03 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 642 TYR 0.013 0.002 TYR B1045 PHE 0.016 0.002 PHE B 683 TRP 0.012 0.002 TRP B 660 HIS 0.008 0.002 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00615 ( 8262) covalent geometry : angle 0.68169 (11222) hydrogen bonds : bond 0.03745 ( 394) hydrogen bonds : angle 5.21856 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 400 GLN cc_start: 0.9612 (tm-30) cc_final: 0.9340 (tm-30) REVERT: B 475 MET cc_start: 0.9498 (mmm) cc_final: 0.9205 (mmm) REVERT: B 649 PHE cc_start: 0.9445 (m-80) cc_final: 0.8773 (m-80) REVERT: B 844 MET cc_start: 0.8819 (ptp) cc_final: 0.8494 (mtp) REVERT: B 871 LYS cc_start: 0.9674 (mmmt) cc_final: 0.9465 (mmmt) REVERT: B 872 MET cc_start: 0.9567 (ttt) cc_final: 0.9184 (tpp) outliers start: 15 outliers final: 14 residues processed: 43 average time/residue: 0.0857 time to fit residues: 5.5653 Evaluate side-chains 44 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 687 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 971 PHE Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 997 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.2814 r_free = 0.2814 target = 0.029500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.022907 restraints weight = 82094.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.023631 restraints weight = 53931.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.024186 restraints weight = 40246.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.024577 restraints weight = 32093.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.024947 restraints weight = 26976.464| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8262 Z= 0.102 Angle : 0.576 9.982 11222 Z= 0.286 Chirality : 0.041 0.292 1268 Planarity : 0.003 0.036 1430 Dihedral : 6.979 82.675 1150 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.90 % Allowed : 11.53 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.21 (0.28), residues: 1009 helix: 1.92 (0.26), residues: 442 sheet: -0.23 (0.44), residues: 150 loop : 0.09 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 248 TYR 0.010 0.001 TYR B 663 PHE 0.013 0.001 PHE B 826 TRP 0.010 0.001 TRP B 378 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8262) covalent geometry : angle 0.57572 (11222) hydrogen bonds : bond 0.03014 ( 394) hydrogen bonds : angle 4.73707 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 400 GLN cc_start: 0.9594 (tm-30) cc_final: 0.9276 (tm-30) REVERT: B 474 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9011 (mt-10) REVERT: B 475 MET cc_start: 0.9466 (mmm) cc_final: 0.9156 (mmm) REVERT: B 649 PHE cc_start: 0.9383 (m-80) cc_final: 0.8729 (m-80) REVERT: B 844 MET cc_start: 0.8770 (ptp) cc_final: 0.8425 (mtp) REVERT: B 871 LYS cc_start: 0.9665 (mmmt) cc_final: 0.9421 (mmmt) REVERT: B 872 MET cc_start: 0.9502 (ttt) cc_final: 0.9107 (tpp) REVERT: B 998 MET cc_start: 0.5745 (ppp) cc_final: 0.5155 (ppp) outliers start: 8 outliers final: 8 residues processed: 37 average time/residue: 0.0874 time to fit residues: 5.1576 Evaluate side-chains 39 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 971 PHE Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 992 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.2812 r_free = 0.2812 target = 0.029342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.022709 restraints weight = 83026.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.023464 restraints weight = 54029.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.024016 restraints weight = 39818.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.024426 restraints weight = 31764.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.024715 restraints weight = 26669.489| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8262 Z= 0.117 Angle : 0.557 9.704 11222 Z= 0.279 Chirality : 0.040 0.302 1268 Planarity : 0.003 0.034 1430 Dihedral : 6.888 82.741 1150 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.90 % Allowed : 11.65 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % 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: 1.36 (0.28), residues: 1009 helix: 2.05 (0.26), residues: 435 sheet: -0.15 (0.44), residues: 150 loop : 0.19 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1004 TYR 0.010 0.001 TYR B 663 PHE 0.012 0.001 PHE B 656 TRP 0.007 0.001 TRP B 378 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8262) covalent geometry : angle 0.55656 (11222) hydrogen bonds : bond 0.02957 ( 394) hydrogen bonds : angle 4.72721 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1212.93 seconds wall clock time: 21 minutes 56.59 seconds (1316.59 seconds total)