Starting phenix.real_space_refine on Fri Aug 22 19:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhl_34803/08_2025/8hhl_34803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhl_34803/08_2025/8hhl_34803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2025/8hhl_34803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2025/8hhl_34803.map" model { file = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2025/8hhl_34803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2025/8hhl_34803.cif" } resolution = 2.87 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 ------------------------------------------------------------------------------- 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= -0.012 sd= 0.253 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 111 5.49 5 Mg 3 5.21 5 S 19 5.16 5 C 3939 2.51 5 N 1321 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6971 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1066 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 28, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 43} Chain: "C" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 624 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 647 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4630 Classifications: {'peptide': 592} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 567} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6663 SG CYS A 552 87.861 24.922 31.530 1.00120.60 S ATOM 6796 SG CYS A 569 84.715 23.574 29.746 1.00120.99 S ATOM 6814 SG CYS A 572 86.921 21.084 31.118 1.00121.86 S Time building chain proxies: 1.95, per 1000 atoms: 0.28 Number of scatterers: 6971 At special positions: 0 Unit cell: (101.094, 89.474, 103.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 111 15.00 Mg 3 11.99 O 1577 8.00 N 1321 7.00 C 3939 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: 0.72 Conformation dependent library (CDL) restraints added in 330.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 569 " Number of angles added : 3 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 58.1% alpha, 14.4% beta 40 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 18 through 52 Processing helix chain 'A' and resid 53 through 85 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.558A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 176 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.605A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 362 through 397 removed outlier: 4.195A pdb=" N GLU A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.230A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 479 removed outlier: 3.520A pdb=" N TRP A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 500 removed outlier: 4.495A pdb=" N MET A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.570A pdb=" N LEU A 563 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 579 through 591 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.076A pdb=" N ILE A 278 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG A 301 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 280 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY A 253 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 262 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A 251 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 264 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 266 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR A 247 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360 removed outlier: 4.813A pdb=" N THR A 327 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG A 321 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 329 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 567 through 568 300 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1580 1.33 - 1.45: 2077 1.45 - 1.57: 3432 1.57 - 1.69: 219 1.69 - 1.81: 31 Bond restraints: 7339 Sorted by residual: bond pdb=" C3' DG D -9 " pdb=" O3' DG D -9 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DT D -10 " pdb=" O3' DT D -10 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" C2' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 1.525 1.504 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CA ASP A 560 " pdb=" CB ASP A 560 " ideal model delta sigma weight residual 1.532 1.547 -0.015 1.51e-02 4.39e+03 9.66e-01 bond pdb=" O4' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.01e-01 ... (remaining 7334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 10112 1.18 - 2.36: 291 2.36 - 3.55: 57 3.55 - 4.73: 8 4.73 - 5.91: 2 Bond angle restraints: 10470 Sorted by residual: angle pdb=" C2' DG D 0 " pdb=" C1' DG D 0 " pdb=" N9 DG D 0 " ideal model delta sigma weight residual 113.50 117.07 -3.57 1.50e+00 4.44e-01 5.66e+00 angle pdb=" C ASP A 559 " pdb=" N ASP A 560 " pdb=" CA ASP A 560 " ideal model delta sigma weight residual 122.61 126.22 -3.61 1.56e+00 4.11e-01 5.36e+00 angle pdb=" C4' DG D 0 " pdb=" O4' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 109.70 106.45 3.25 1.50e+00 4.44e-01 4.70e+00 angle pdb=" CA ASP A 560 " pdb=" CB ASP A 560 " pdb=" CG ASP A 560 " ideal model delta sigma weight residual 112.60 114.65 -2.05 1.00e+00 1.00e+00 4.21e+00 angle pdb=" OP2 DT D -8 " pdb=" P DT D -8 " pdb=" O5' DT D -8 " ideal model delta sigma weight residual 108.00 102.09 5.91 3.00e+00 1.11e-01 3.88e+00 ... (remaining 10465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 3630 23.75 - 47.50: 449 47.50 - 71.25: 226 71.25 - 95.00: 19 95.00 - 118.75: 1 Dihedral angle restraints: 4325 sinusoidal: 2602 harmonic: 1723 Sorted by residual: dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -172.34 66.34 1 1.70e+01 3.46e-03 1.99e+01 dihedral pdb=" C4' DG D -9 " pdb=" C3' DG D -9 " pdb=" O3' DG D -9 " pdb=" P DT D -8 " ideal model delta sinusoidal sigma weight residual 220.00 101.25 118.75 1 3.50e+01 8.16e-04 1.16e+01 dihedral pdb=" CA ASP A 477 " pdb=" CB ASP A 477 " pdb=" CG ASP A 477 " pdb=" OD1 ASP A 477 " ideal model delta sinusoidal sigma weight residual -30.00 -86.97 56.97 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 4322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 889 0.033 - 0.066: 241 0.066 - 0.099: 58 0.099 - 0.133: 17 0.133 - 0.166: 5 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C1' DG D 0 " pdb=" O4' DG D 0 " pdb=" C2' DG D 0 " pdb=" N9 DG D 0 " both_signs ideal model delta sigma weight residual False 2.42 2.25 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ASP A 560 " pdb=" N ASP A 560 " pdb=" C ASP A 560 " pdb=" CB ASP A 560 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1207 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG D 0 " 0.027 2.00e-02 2.50e+03 1.15e-02 3.97e+00 pdb=" N9 DG D 0 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DG D 0 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG D 0 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG D 0 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG D 0 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG D 0 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG D 0 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG D 0 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG D 0 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG D 0 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG D 0 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 2 " 0.025 2.00e-02 2.50e+03 1.06e-02 3.34e+00 pdb=" N9 G B 2 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G B 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 2 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 2 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 2 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 2 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C GLN A 452 " -0.031 2.00e-02 2.50e+03 pdb=" O GLN A 452 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 453 " 0.010 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 215 2.68 - 3.24: 6117 3.24 - 3.79: 12497 3.79 - 4.35: 16282 4.35 - 4.90: 24625 Nonbonded interactions: 59736 Sorted by model distance: nonbonded pdb=" OD1 ASP A 579 " pdb="MG MG A 601 " model vdw 2.126 2.170 nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 2.134 2.170 nonbonded pdb=" OP1 DG D 15 " pdb="MG MG A 601 " model vdw 2.143 2.170 nonbonded pdb=" OG SER A 334 " pdb=" O ALA A 336 " model vdw 2.154 3.040 nonbonded pdb=" NE2 HIS A 317 " pdb="MG MG A 601 " model vdw 2.198 2.250 ... (remaining 59731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.062 7343 Z= 0.172 Angle : 0.513 9.011 10473 Z= 0.285 Chirality : 0.035 0.166 1210 Planarity : 0.004 0.042 951 Dihedral : 22.356 118.750 3205 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.29 % Allowed : 12.29 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.35), residues: 590 helix: 2.63 (0.29), residues: 323 sheet: 1.62 (0.63), residues: 60 loop : -0.37 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.010 0.001 TYR A 42 PHE 0.006 0.001 PHE A 443 TRP 0.008 0.001 TRP A 232 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7339) covalent geometry : angle 0.49870 (10470) hydrogen bonds : bond 0.12160 ( 405) hydrogen bonds : angle 5.09844 ( 1085) metal coordination : bond 0.03038 ( 4) metal coordination : angle 7.17526 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.167 Fit side-chains REVERT: A 63 MET cc_start: 0.8112 (ttt) cc_final: 0.7844 (ttp) REVERT: A 160 ASP cc_start: 0.7952 (m-30) cc_final: 0.7678 (m-30) REVERT: A 172 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7002 (mm-40) REVERT: A 199 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7586 (tt0) REVERT: A 264 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8790 (mt) REVERT: A 404 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7712 (p0) REVERT: A 416 LYS cc_start: 0.6723 (mttt) cc_final: 0.5308 (tttm) REVERT: A 458 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7644 (mmm-85) REVERT: A 575 MET cc_start: 0.8659 (mtp) cc_final: 0.8283 (mtt) outliers start: 11 outliers final: 2 residues processed: 82 average time/residue: 0.8500 time to fit residues: 72.1803 Evaluate side-chains 51 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 404 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 242 GLN A 478 GLN A 556 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.137477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105045 restraints weight = 9787.875| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.51 r_work: 0.3215 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7343 Z= 0.181 Angle : 0.545 8.594 10473 Z= 0.302 Chirality : 0.037 0.158 1210 Planarity : 0.005 0.098 951 Dihedral : 23.847 117.599 2123 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.12 % Allowed : 17.08 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.34), residues: 590 helix: 3.10 (0.28), residues: 324 sheet: 1.85 (0.62), residues: 60 loop : -0.22 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 580 TYR 0.009 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7339) covalent geometry : angle 0.54482 (10470) hydrogen bonds : bond 0.04721 ( 405) hydrogen bonds : angle 3.56205 ( 1085) metal coordination : bond 0.00216 ( 4) metal coordination : angle 0.87394 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.171 Fit side-chains REVERT: A 63 MET cc_start: 0.8303 (ttt) cc_final: 0.8023 (ttp) REVERT: A 89 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 146 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8085 (mtm-85) REVERT: A 199 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7811 (tt0) REVERT: A 325 GLU cc_start: 0.8349 (mp0) cc_final: 0.8148 (mp0) REVERT: A 416 LYS cc_start: 0.6777 (mttt) cc_final: 0.5453 (tttm) REVERT: A 458 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8345 (mmm-85) REVERT: A 498 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6610 (pm20) REVERT: A 575 MET cc_start: 0.8599 (mtp) cc_final: 0.8233 (mtt) outliers start: 15 outliers final: 6 residues processed: 62 average time/residue: 0.9196 time to fit residues: 58.9294 Evaluate side-chains 51 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103848 restraints weight = 9848.916| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.51 r_work: 0.3178 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7343 Z= 0.222 Angle : 0.563 8.239 10473 Z= 0.309 Chirality : 0.038 0.165 1210 Planarity : 0.005 0.050 951 Dihedral : 23.849 116.919 2118 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.79 % Allowed : 17.08 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.34), residues: 590 helix: 3.07 (0.27), residues: 324 sheet: 1.53 (0.60), residues: 62 loop : -0.22 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 85 TYR 0.009 0.001 TYR A 42 PHE 0.007 0.001 PHE A 443 TRP 0.012 0.001 TRP A 232 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 7339) covalent geometry : angle 0.56296 (10470) hydrogen bonds : bond 0.04969 ( 405) hydrogen bonds : angle 3.59315 ( 1085) metal coordination : bond 0.00329 ( 4) metal coordination : angle 0.82634 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.209 Fit side-chains REVERT: A 63 MET cc_start: 0.8317 (ttt) cc_final: 0.8051 (ttp) REVERT: A 160 ASP cc_start: 0.7940 (m-30) cc_final: 0.7722 (m-30) REVERT: A 199 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7811 (tp40) REVERT: A 416 LYS cc_start: 0.6699 (mttt) cc_final: 0.5313 (tttm) REVERT: A 458 ARG cc_start: 0.8718 (mmm160) cc_final: 0.8344 (mmm-85) REVERT: A 498 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: A 575 MET cc_start: 0.8605 (mtp) cc_final: 0.8235 (mtt) outliers start: 23 outliers final: 8 residues processed: 61 average time/residue: 0.8899 time to fit residues: 56.2603 Evaluate side-chains 51 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.102431 restraints weight = 9905.094| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.52 r_work: 0.3177 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7343 Z= 0.235 Angle : 0.568 7.852 10473 Z= 0.314 Chirality : 0.039 0.168 1210 Planarity : 0.004 0.042 951 Dihedral : 23.876 116.833 2118 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.75 % Allowed : 18.12 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.34), residues: 590 helix: 3.00 (0.27), residues: 324 sheet: 1.45 (0.61), residues: 62 loop : -0.21 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.010 0.001 TYR A 42 PHE 0.007 0.001 PHE A 443 TRP 0.012 0.001 TRP A 232 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 7339) covalent geometry : angle 0.56762 (10470) hydrogen bonds : bond 0.05032 ( 405) hydrogen bonds : angle 3.58159 ( 1085) metal coordination : bond 0.00295 ( 4) metal coordination : angle 0.82244 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.177 Fit side-chains REVERT: A 63 MET cc_start: 0.8339 (ttt) cc_final: 0.8080 (ttp) REVERT: A 160 ASP cc_start: 0.8031 (m-30) cc_final: 0.7794 (m-30) REVERT: A 335 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8809 (t0) REVERT: A 367 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7830 (ttp-110) REVERT: A 416 LYS cc_start: 0.6735 (mttt) cc_final: 0.5353 (tttm) REVERT: A 458 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8364 (mmm-85) REVERT: A 498 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: A 575 MET cc_start: 0.8600 (mtp) cc_final: 0.8253 (mtt) outliers start: 18 outliers final: 10 residues processed: 60 average time/residue: 0.8020 time to fit residues: 49.9721 Evaluate side-chains 55 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104916 restraints weight = 9837.953| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.51 r_work: 0.3221 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7343 Z= 0.157 Angle : 0.520 8.216 10473 Z= 0.289 Chirality : 0.035 0.146 1210 Planarity : 0.004 0.036 951 Dihedral : 23.797 114.005 2118 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.96 % Allowed : 18.54 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.34), residues: 590 helix: 3.25 (0.27), residues: 324 sheet: 1.44 (0.60), residues: 62 loop : -0.21 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.008 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.011 0.001 TRP A 232 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7339) covalent geometry : angle 0.51972 (10470) hydrogen bonds : bond 0.04288 ( 405) hydrogen bonds : angle 3.35095 ( 1085) metal coordination : bond 0.00137 ( 4) metal coordination : angle 0.58898 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.176 Fit side-chains REVERT: A 63 MET cc_start: 0.8313 (ttt) cc_final: 0.8015 (ttp) REVERT: A 98 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7705 (mtm-85) REVERT: A 146 ARG cc_start: 0.8581 (mtp85) cc_final: 0.7982 (mtm-85) REVERT: A 160 ASP cc_start: 0.8072 (m-30) cc_final: 0.7827 (m-30) REVERT: A 413 LYS cc_start: 0.8087 (tttt) cc_final: 0.7099 (tptp) REVERT: A 416 LYS cc_start: 0.6654 (mttt) cc_final: 0.5319 (tttm) REVERT: A 458 ARG cc_start: 0.8757 (mmm160) cc_final: 0.8359 (mmm-85) REVERT: A 498 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6365 (pm20) REVERT: A 575 MET cc_start: 0.8577 (mtp) cc_final: 0.8223 (mtt) outliers start: 19 outliers final: 9 residues processed: 59 average time/residue: 0.7416 time to fit residues: 45.4159 Evaluate side-chains 53 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102820 restraints weight = 9927.535| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.50 r_work: 0.3180 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7343 Z= 0.228 Angle : 0.568 8.848 10473 Z= 0.311 Chirality : 0.038 0.160 1210 Planarity : 0.004 0.037 951 Dihedral : 23.851 114.173 2118 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.54 % Allowed : 19.38 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.34), residues: 590 helix: 3.07 (0.27), residues: 324 sheet: 1.38 (0.60), residues: 62 loop : -0.32 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.009 0.001 TYR A 42 PHE 0.008 0.001 PHE A 443 TRP 0.011 0.001 TRP A 232 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 7339) covalent geometry : angle 0.56799 (10470) hydrogen bonds : bond 0.04818 ( 405) hydrogen bonds : angle 3.49007 ( 1085) metal coordination : bond 0.00253 ( 4) metal coordination : angle 0.74925 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.182 Fit side-chains REVERT: A 63 MET cc_start: 0.8319 (ttt) cc_final: 0.8065 (ttp) REVERT: A 160 ASP cc_start: 0.8053 (m-30) cc_final: 0.7792 (m-30) REVERT: A 335 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8824 (t0) REVERT: A 367 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7866 (ttp-110) REVERT: A 413 LYS cc_start: 0.8126 (tttt) cc_final: 0.7128 (tptp) REVERT: A 416 LYS cc_start: 0.6699 (mttt) cc_final: 0.5302 (tttm) REVERT: A 458 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8370 (mmm-85) REVERT: A 498 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6597 (pm20) REVERT: A 575 MET cc_start: 0.8587 (mtp) cc_final: 0.8238 (mtt) outliers start: 17 outliers final: 9 residues processed: 57 average time/residue: 0.7528 time to fit residues: 44.5503 Evaluate side-chains 54 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.135198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103005 restraints weight = 9863.406| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.48 r_work: 0.3187 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7343 Z= 0.214 Angle : 0.558 6.586 10473 Z= 0.309 Chirality : 0.038 0.158 1210 Planarity : 0.004 0.037 951 Dihedral : 23.895 114.139 2118 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.96 % Allowed : 19.17 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.34), residues: 590 helix: 3.09 (0.27), residues: 324 sheet: 1.39 (0.61), residues: 62 loop : -0.36 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.009 0.001 TYR A 42 PHE 0.007 0.001 PHE A 443 TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 7339) covalent geometry : angle 0.55826 (10470) hydrogen bonds : bond 0.04814 ( 405) hydrogen bonds : angle 3.47558 ( 1085) metal coordination : bond 0.00242 ( 4) metal coordination : angle 0.81873 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.134 Fit side-chains REVERT: A 63 MET cc_start: 0.8294 (ttt) cc_final: 0.8046 (ttp) REVERT: A 160 ASP cc_start: 0.8063 (m-30) cc_final: 0.7801 (m-30) REVERT: A 335 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8829 (t0) REVERT: A 367 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7882 (ttp-110) REVERT: A 413 LYS cc_start: 0.8131 (tttt) cc_final: 0.7150 (tptp) REVERT: A 416 LYS cc_start: 0.6705 (mttt) cc_final: 0.5330 (tttm) REVERT: A 458 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8363 (mmm-85) REVERT: A 575 MET cc_start: 0.8578 (mtp) cc_final: 0.8238 (mtt) outliers start: 19 outliers final: 11 residues processed: 59 average time/residue: 0.8103 time to fit residues: 49.5434 Evaluate side-chains 55 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.137818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105391 restraints weight = 9470.298| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.42 r_work: 0.3277 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7343 Z= 0.193 Angle : 0.553 9.049 10473 Z= 0.304 Chirality : 0.037 0.151 1210 Planarity : 0.004 0.037 951 Dihedral : 23.913 112.648 2118 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.54 % Allowed : 20.21 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.34), residues: 590 helix: 3.16 (0.27), residues: 324 sheet: 1.35 (0.60), residues: 62 loop : -0.33 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.009 0.001 TYR A 42 PHE 0.007 0.001 PHE A 443 TRP 0.012 0.001 TRP A 232 HIS 0.002 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7339) covalent geometry : angle 0.55284 (10470) hydrogen bonds : bond 0.04607 ( 405) hydrogen bonds : angle 3.42210 ( 1085) metal coordination : bond 0.00221 ( 4) metal coordination : angle 0.76935 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.215 Fit side-chains REVERT: A 63 MET cc_start: 0.8337 (ttt) cc_final: 0.8093 (ttp) REVERT: A 160 ASP cc_start: 0.8003 (m-30) cc_final: 0.7748 (m-30) REVERT: A 335 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8806 (t0) REVERT: A 367 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7878 (ttp-110) REVERT: A 413 LYS cc_start: 0.8152 (tttt) cc_final: 0.7188 (tptp) REVERT: A 416 LYS cc_start: 0.6651 (mttt) cc_final: 0.5362 (tttm) REVERT: A 458 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8385 (mmm-85) REVERT: A 575 MET cc_start: 0.8525 (mtp) cc_final: 0.8210 (mtt) outliers start: 17 outliers final: 9 residues processed: 59 average time/residue: 0.7704 time to fit residues: 47.2434 Evaluate side-chains 55 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 0.0370 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.138299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106108 restraints weight = 9453.886| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.40 r_work: 0.3306 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7343 Z= 0.160 Angle : 0.543 9.641 10473 Z= 0.298 Chirality : 0.036 0.210 1210 Planarity : 0.004 0.036 951 Dihedral : 23.813 111.079 2118 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.50 % Allowed : 21.67 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.34), residues: 590 helix: 3.25 (0.27), residues: 324 sheet: 1.36 (0.60), residues: 62 loop : -0.29 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 98 TYR 0.007 0.001 TYR A 42 PHE 0.006 0.001 PHE A 443 TRP 0.011 0.001 TRP A 232 HIS 0.003 0.000 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7339) covalent geometry : angle 0.54280 (10470) hydrogen bonds : bond 0.04256 ( 405) hydrogen bonds : angle 3.31743 ( 1085) metal coordination : bond 0.00158 ( 4) metal coordination : angle 0.60351 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.212 Fit side-chains REVERT: A 63 MET cc_start: 0.8310 (ttt) cc_final: 0.8080 (ttp) REVERT: A 98 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7651 (mtm-85) REVERT: A 367 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7843 (ttp-110) REVERT: A 413 LYS cc_start: 0.8003 (tttt) cc_final: 0.7042 (tptp) REVERT: A 416 LYS cc_start: 0.6637 (mttt) cc_final: 0.5357 (tttm) REVERT: A 458 ARG cc_start: 0.8728 (mmm160) cc_final: 0.8358 (mmm-85) REVERT: A 575 MET cc_start: 0.8541 (mtp) cc_final: 0.8218 (mtt) outliers start: 12 outliers final: 8 residues processed: 55 average time/residue: 0.7782 time to fit residues: 44.3564 Evaluate side-chains 54 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.141665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109397 restraints weight = 9693.200| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.49 r_work: 0.3303 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7343 Z= 0.126 Angle : 0.523 10.802 10473 Z= 0.285 Chirality : 0.033 0.141 1210 Planarity : 0.004 0.034 951 Dihedral : 23.609 106.899 2118 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.67 % Allowed : 23.54 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.34), residues: 590 helix: 3.42 (0.27), residues: 324 sheet: 1.40 (0.60), residues: 62 loop : -0.25 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.005 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.013 0.001 TRP A 50 HIS 0.002 0.000 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7339) covalent geometry : angle 0.52288 (10470) hydrogen bonds : bond 0.03643 ( 405) hydrogen bonds : angle 3.11550 ( 1085) metal coordination : bond 0.00075 ( 4) metal coordination : angle 0.44794 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.8202 (ttt) cc_final: 0.7963 (ttp) REVERT: A 413 LYS cc_start: 0.7798 (tttt) cc_final: 0.6851 (tptp) REVERT: A 416 LYS cc_start: 0.6583 (mttt) cc_final: 0.5253 (tttm) REVERT: A 458 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8298 (mmm-85) REVERT: A 575 MET cc_start: 0.8512 (mtp) cc_final: 0.8177 (mtt) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.6549 time to fit residues: 40.3129 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 33 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106869 restraints weight = 9749.089| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.49 r_work: 0.3262 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7343 Z= 0.150 Angle : 0.545 14.656 10473 Z= 0.294 Chirality : 0.034 0.140 1210 Planarity : 0.004 0.045 951 Dihedral : 23.642 107.038 2118 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.29 % Allowed : 23.54 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.34), residues: 590 helix: 3.35 (0.27), residues: 324 sheet: 1.36 (0.60), residues: 62 loop : -0.23 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 367 TYR 0.007 0.001 TYR A 42 PHE 0.007 0.001 PHE A 443 TRP 0.011 0.001 TRP A 232 HIS 0.001 0.000 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7339) covalent geometry : angle 0.54482 (10470) hydrogen bonds : bond 0.03880 ( 405) hydrogen bonds : angle 3.16998 ( 1085) metal coordination : bond 0.00121 ( 4) metal coordination : angle 0.49319 ( 3) =============================================================================== Job complete usr+sys time: 2267.64 seconds wall clock time: 39 minutes 14.04 seconds (2354.04 seconds total)