Starting phenix.real_space_refine on Wed Feb 12 04:15:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhl_34803/02_2025/8hhl_34803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhl_34803/02_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_34803/02_2025/8hhl_34803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhl_34803/02_2025/8hhl_34803.map" model { file = "/net/cci-nas-00/data/ceres_data/8hhl_34803/02_2025/8hhl_34803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhl_34803/02_2025/8hhl_34803.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.69, per 1000 atoms: 0.67 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: 2.49 Conformation dependent library (CDL) restraints added in 604.0 milliseconds 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: 2.78 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: 3.04 Time building geometry restraints manager: 2.74 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: 0.070 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- 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 7339 Z= 0.217 Angle : 0.499 5.911 10470 Z= 0.284 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP A 232 HIS 0.002 0.000 HIS A 12 PHE 0.006 0.001 PHE A 443 TYR 0.010 0.001 TYR A 42 ARG 0.002 0.000 ARG A 185 *********************** 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 : 0.672 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: 1.7103 time to fit residues: 145.7754 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 : 0.606 ------------------------------------------------------------------------------- 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 58 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.0670 chunk 40 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.136410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104151 restraints weight = 9684.598| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.49 r_work: 0.3198 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7339 Z= 0.287 Angle : 0.568 8.791 10470 Z= 0.314 Chirality : 0.038 0.167 1210 Planarity : 0.006 0.111 951 Dihedral : 23.885 118.296 2123 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.54 % Allowed : 16.88 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.34), residues: 590 helix: 3.07 (0.28), residues: 323 sheet: 1.81 (0.62), residues: 60 loop : -0.30 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.003 0.001 HIS A 12 PHE 0.006 0.001 PHE A 443 TYR 0.009 0.001 TYR A 42 ARG 0.006 0.001 ARG A 580 *********************** 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: 17 poor density : 49 time to evaluate : 0.597 Fit side-chains REVERT: A 63 MET cc_start: 0.8332 (ttt) cc_final: 0.8067 (ttp) REVERT: A 89 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8188 (pp) REVERT: A 103 ARG cc_start: 0.8329 (mtp180) cc_final: 0.8049 (mtm180) REVERT: A 160 ASP cc_start: 0.7987 (m-30) cc_final: 0.7706 (m-30) REVERT: A 172 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7442 (mm-40) REVERT: A 199 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7813 (tt0) REVERT: A 325 GLU cc_start: 0.8339 (mp0) cc_final: 0.8130 (mp0) REVERT: A 416 LYS cc_start: 0.6804 (mttt) cc_final: 0.5464 (tttm) REVERT: A 458 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8345 (mmm-85) REVERT: A 459 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8074 (mttp) REVERT: A 498 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: A 575 MET cc_start: 0.8607 (mtp) cc_final: 0.8221 (mtt) outliers start: 17 outliers final: 8 residues processed: 62 average time/residue: 1.9275 time to fit residues: 124.0298 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 89 ILE Chi-restraints excluded: chain A residue 93 LEU 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 459 LYS 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 43 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.134055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101734 restraints weight = 9869.703| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.52 r_work: 0.3162 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7339 Z= 0.370 Angle : 0.597 8.420 10470 Z= 0.327 Chirality : 0.041 0.180 1210 Planarity : 0.005 0.083 951 Dihedral : 23.946 118.289 2119 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.96 % Allowed : 18.12 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.34), residues: 590 helix: 2.89 (0.27), residues: 324 sheet: 1.55 (0.61), residues: 62 loop : -0.29 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 232 HIS 0.003 0.001 HIS A 12 PHE 0.007 0.002 PHE A 443 TYR 0.010 0.002 TYR A 42 ARG 0.007 0.001 ARG A 580 *********************** 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 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.8341 (ttt) cc_final: 0.8085 (ttp) REVERT: A 103 ARG cc_start: 0.8307 (mtp180) cc_final: 0.8017 (mtm180) REVERT: A 172 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7515 (mm-40) REVERT: A 199 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7861 (tp40) REVERT: A 335 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8796 (t0) REVERT: A 416 LYS cc_start: 0.6808 (mttt) cc_final: 0.5378 (tttm) REVERT: A 458 ARG cc_start: 0.8730 (mmm160) cc_final: 0.8381 (mmm-85) REVERT: A 459 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8090 (mttp) REVERT: A 498 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: A 575 MET cc_start: 0.8592 (mtp) cc_final: 0.8244 (mtt) outliers start: 19 outliers final: 8 residues processed: 60 average time/residue: 1.8689 time to fit residues: 116.4262 Evaluate side-chains 55 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 304 ASP 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 560 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.134992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102723 restraints weight = 9936.813| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.50 r_work: 0.3191 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7339 Z= 0.278 Angle : 0.551 7.890 10470 Z= 0.305 Chirality : 0.038 0.163 1210 Planarity : 0.004 0.054 951 Dihedral : 23.895 116.658 2119 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.17 % Allowed : 18.54 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.34), residues: 590 helix: 3.06 (0.27), residues: 324 sheet: 1.47 (0.61), residues: 62 loop : -0.30 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.002 0.001 HIS A 12 PHE 0.006 0.001 PHE A 443 TYR 0.009 0.001 TYR A 42 ARG 0.004 0.000 ARG A 85 *********************** 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 68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.8332 (ttt) cc_final: 0.8078 (ttp) REVERT: A 103 ARG cc_start: 0.8317 (mtp180) cc_final: 0.8035 (mtm180) REVERT: A 172 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7498 (mm-40) REVERT: A 416 LYS cc_start: 0.6765 (mttt) cc_final: 0.5403 (tttm) REVERT: A 458 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8349 (mmm-85) REVERT: A 459 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8064 (mttp) REVERT: A 575 MET cc_start: 0.8552 (mtp) cc_final: 0.8234 (mtt) outliers start: 20 outliers final: 11 residues processed: 62 average time/residue: 1.7561 time to fit residues: 113.3584 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 93 LEU 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 340 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 16 optimal weight: 20.0000 chunk 40 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 0.0770 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.141641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109491 restraints weight = 9766.204| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.51 r_work: 0.3298 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7339 Z= 0.154 Angle : 0.492 7.179 10470 Z= 0.276 Chirality : 0.034 0.142 1210 Planarity : 0.004 0.036 951 Dihedral : 23.714 110.727 2118 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.92 % Allowed : 19.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.35), residues: 590 helix: 3.49 (0.27), residues: 324 sheet: 1.53 (0.60), residues: 62 loop : -0.13 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.002 0.000 HIS A 463 PHE 0.005 0.001 PHE A 155 TYR 0.005 0.001 TYR A 42 ARG 0.004 0.000 ARG A 499 *********************** 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 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.604 Fit side-chains REVERT: A 63 MET cc_start: 0.8244 (ttt) cc_final: 0.7984 (ttp) REVERT: A 89 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8020 (pp) REVERT: A 146 ARG cc_start: 0.8534 (mtp85) cc_final: 0.7993 (mtm-85) REVERT: A 172 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7288 (mm-40) REVERT: A 413 LYS cc_start: 0.7877 (tttt) cc_final: 0.6871 (tptp) REVERT: A 416 LYS cc_start: 0.6605 (mttt) cc_final: 0.5259 (tttm) REVERT: A 458 ARG cc_start: 0.8754 (mmm160) cc_final: 0.8318 (mmm-85) REVERT: A 459 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7978 (mttp) REVERT: A 575 MET cc_start: 0.8561 (mtp) cc_final: 0.8230 (mtt) outliers start: 14 outliers final: 5 residues processed: 61 average time/residue: 1.8154 time to fit residues: 115.2342 Evaluate side-chains 52 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 ILE 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 459 LYS 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 62 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.135456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103157 restraints weight = 9832.834| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.48 r_work: 0.3211 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7339 Z= 0.263 Angle : 0.543 9.334 10470 Z= 0.298 Chirality : 0.037 0.158 1210 Planarity : 0.004 0.071 951 Dihedral : 23.780 111.648 2118 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.54 % Allowed : 20.00 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.34), residues: 590 helix: 3.32 (0.27), residues: 324 sheet: 1.43 (0.61), residues: 62 loop : -0.19 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 232 HIS 0.002 0.001 HIS A 12 PHE 0.007 0.001 PHE A 443 TYR 0.008 0.001 TYR A 42 ARG 0.004 0.000 ARG A 85 *********************** 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 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.632 Fit side-chains REVERT: A 63 MET cc_start: 0.8320 (ttt) cc_final: 0.8014 (ttp) REVERT: A 88 LYS cc_start: 0.8687 (tmmt) cc_final: 0.8381 (tppt) REVERT: A 172 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7473 (mm-40) REVERT: A 413 LYS cc_start: 0.8080 (tttt) cc_final: 0.7096 (tptp) REVERT: A 416 LYS cc_start: 0.6683 (mttt) cc_final: 0.5294 (tttm) REVERT: A 458 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8318 (mmm-85) REVERT: A 459 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8068 (mttp) REVERT: A 575 MET cc_start: 0.8569 (mtp) cc_final: 0.8233 (mtt) outliers start: 17 outliers final: 9 residues processed: 61 average time/residue: 1.7679 time to fit residues: 112.3119 Evaluate side-chains 54 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain A residue 264 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.131353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099113 restraints weight = 9884.527| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.54 r_work: 0.3148 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 7339 Z= 0.484 Angle : 0.664 9.169 10470 Z= 0.358 Chirality : 0.044 0.181 1210 Planarity : 0.006 0.071 951 Dihedral : 24.059 116.968 2118 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.54 % Allowed : 20.42 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.33), residues: 590 helix: 2.69 (0.26), residues: 324 sheet: 1.41 (0.61), residues: 62 loop : -0.41 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 232 HIS 0.004 0.001 HIS A 12 PHE 0.008 0.002 PHE A 443 TYR 0.013 0.002 TYR A 42 ARG 0.004 0.001 ARG A 85 *********************** 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 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.595 Fit side-chains REVERT: A 98 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7766 (mtm-85) REVERT: A 172 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7640 (mm110) REVERT: A 335 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8890 (t0) REVERT: A 416 LYS cc_start: 0.6843 (mttt) cc_final: 0.5443 (tttm) REVERT: A 458 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8329 (mmm-85) REVERT: A 459 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8119 (mttp) REVERT: A 575 MET cc_start: 0.8588 (mtp) cc_final: 0.8274 (mtt) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 1.8956 time to fit residues: 114.2369 Evaluate side-chains 51 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 ASP 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 53 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.138007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105812 restraints weight = 9445.277| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.40 r_work: 0.3288 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7339 Z= 0.221 Angle : 0.544 6.873 10470 Z= 0.302 Chirality : 0.036 0.146 1210 Planarity : 0.004 0.062 951 Dihedral : 23.943 114.175 2118 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.71 % Allowed : 21.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.34), residues: 590 helix: 3.14 (0.27), residues: 324 sheet: 1.36 (0.60), residues: 62 loop : -0.32 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 12 PHE 0.006 0.001 PHE A 155 TYR 0.008 0.001 TYR A 42 ARG 0.003 0.000 ARG A 85 *********************** 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 60 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.622 Fit side-chains REVERT: A 88 LYS cc_start: 0.8613 (tmmt) cc_final: 0.8348 (tppt) REVERT: A 98 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7912 (mtm-85) REVERT: A 172 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7492 (mm-40) REVERT: A 335 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8774 (t0) REVERT: A 413 LYS cc_start: 0.8175 (tttt) cc_final: 0.7218 (tptp) REVERT: A 416 LYS cc_start: 0.6622 (mttt) cc_final: 0.5355 (tttm) REVERT: A 458 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8356 (mmm-85) REVERT: A 459 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8078 (mttp) REVERT: A 498 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: A 575 MET cc_start: 0.8544 (mtp) cc_final: 0.8205 (mtt) outliers start: 13 outliers final: 8 residues processed: 56 average time/residue: 1.8600 time to fit residues: 108.2368 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.136680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104401 restraints weight = 9504.500| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.42 r_work: 0.3275 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7339 Z= 0.263 Angle : 0.570 10.964 10470 Z= 0.311 Chirality : 0.037 0.146 1210 Planarity : 0.004 0.062 951 Dihedral : 23.906 112.770 2118 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.92 % Allowed : 21.67 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.34), residues: 590 helix: 3.12 (0.27), residues: 324 sheet: 1.32 (0.60), residues: 62 loop : -0.34 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 12 PHE 0.007 0.001 PHE A 443 TYR 0.009 0.001 TYR A 42 ARG 0.004 0.000 ARG A 85 *********************** 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 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.503 Fit side-chains REVERT: A 88 LYS cc_start: 0.8670 (tmmt) cc_final: 0.8421 (tppt) REVERT: A 98 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7801 (mtm-85) REVERT: A 172 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7503 (mm-40) REVERT: A 335 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8797 (t0) REVERT: A 413 LYS cc_start: 0.8170 (tttt) cc_final: 0.7212 (tptp) REVERT: A 416 LYS cc_start: 0.6656 (mttt) cc_final: 0.5345 (tttm) REVERT: A 458 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8349 (mmm-85) REVERT: A 459 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8098 (mttp) REVERT: A 498 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: A 575 MET cc_start: 0.8543 (mtp) cc_final: 0.8194 (mtt) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 1.8030 time to fit residues: 105.0629 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 93 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.137582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105254 restraints weight = 9542.670| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.40 r_work: 0.3282 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7339 Z= 0.259 Angle : 0.564 10.065 10470 Z= 0.309 Chirality : 0.037 0.191 1210 Planarity : 0.004 0.062 951 Dihedral : 23.834 112.414 2118 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.50 % Allowed : 22.08 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.34), residues: 590 helix: 3.09 (0.27), residues: 324 sheet: 1.34 (0.59), residues: 62 loop : -0.34 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.002 0.001 HIS A 426 PHE 0.006 0.001 PHE A 443 TYR 0.008 0.001 TYR A 42 ARG 0.004 0.000 ARG A 85 ********************** 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 59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.574 Fit side-chains REVERT: A 88 LYS cc_start: 0.8669 (tmmt) cc_final: 0.8429 (tppt) REVERT: A 98 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7733 (mtm-85) REVERT: A 172 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7512 (mm-40) REVERT: A 335 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8746 (t0) REVERT: A 348 MET cc_start: 0.9115 (ttt) cc_final: 0.8885 (ttt) REVERT: A 413 LYS cc_start: 0.8180 (tttt) cc_final: 0.7199 (tptp) REVERT: A 416 LYS cc_start: 0.6640 (mttt) cc_final: 0.5337 (tttm) REVERT: A 458 ARG cc_start: 0.8597 (mmm160) cc_final: 0.8352 (mmm-85) REVERT: A 459 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8105 (mttp) REVERT: A 498 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: A 575 MET cc_start: 0.8549 (mtp) cc_final: 0.8208 (mtt) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 1.9170 time to fit residues: 109.5261 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 93 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 5 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 32 optimal weight: 0.0980 overall best weight: 4.4188 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.137199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104769 restraints weight = 9445.887| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.40 r_work: 0.3267 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7339 Z= 0.297 Angle : 0.596 11.274 10470 Z= 0.322 Chirality : 0.038 0.179 1210 Planarity : 0.005 0.064 951 Dihedral : 23.866 112.970 2118 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.92 % Allowed : 22.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.34), residues: 590 helix: 3.00 (0.27), residues: 324 sheet: 1.35 (0.59), residues: 62 loop : -0.37 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.002 0.001 HIS A 269 PHE 0.008 0.001 PHE A 443 TYR 0.009 0.001 TYR A 42 ARG 0.004 0.000 ARG A 85 =============================================================================== Job complete usr+sys time: 4813.60 seconds wall clock time: 85 minutes 37.16 seconds (5137.16 seconds total)