Starting phenix.real_space_refine on Fri Aug 22 23:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2i_38856/08_2025/8y2i_38856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2i_38856/08_2025/8y2i_38856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y2i_38856/08_2025/8y2i_38856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2i_38856/08_2025/8y2i_38856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y2i_38856/08_2025/8y2i_38856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2i_38856/08_2025/8y2i_38856.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 20 5.16 5 C 4960 2.51 5 N 1577 2.21 5 O 1976 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: 8676 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 5671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5671 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 35, 'TRANS': 687} Chain breaks: 4 Chain: "C" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2208 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 46, 'rna3p_pyr': 46} Link IDs: {'rna2p': 12, 'rna3p': 91} Chain breaks: 1 Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8676 At special positions: 0 Unit cell: (109.08, 93.96, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 143 15.00 O 1976 8.00 N 1577 7.00 C 4960 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: 0.90 Conformation dependent library (CDL) restraints added in 243.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 48.8% alpha, 12.3% beta 43 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.667A pdb=" N HIS A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 81 removed outlier: 3.959A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.657A pdb=" N LYS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.888A pdb=" N TRP A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 162 removed outlier: 4.125A pdb=" N GLY A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.296A pdb=" N LEU A 189 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 removed outlier: 3.708A pdb=" N TRP A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.821A pdb=" N LYS A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 246 through 265 removed outlier: 3.649A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 267 No H-bonds generated for 'chain 'A' and resid 266 through 267' Processing helix chain 'A' and resid 268 through 272 removed outlier: 3.767A pdb=" N LYS A 271 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 272 " --> pdb=" O PHE A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 272' Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 300 through 316 removed outlier: 4.301A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 333 removed outlier: 3.651A pdb=" N LEU A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 350 through 369 Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 379 through 399 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.792A pdb=" N GLU A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 635 through 658 removed outlier: 3.897A pdb=" N ALA A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU A 642 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 698 removed outlier: 3.556A pdb=" N MET A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.552A pdb=" N GLU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 884 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 43 removed outlier: 6.609A pdb=" N ASP A 552 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A 541 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 554 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU A 539 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 556 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 537 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 558 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 455 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 455 removed outlier: 4.835A pdb=" N LEU A 428 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N SER A 475 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N GLY A 426 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 600 removed outlier: 7.262A pdb=" N LEU A 596 " --> pdb=" O ASP A 591 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP A 591 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE A 662 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 575 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA A 664 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N ILE A 577 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 661 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 721 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU A 663 " --> pdb=" O VAL A 721 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1077 1.29 - 1.42: 3154 1.42 - 1.55: 4606 1.55 - 1.68: 280 1.68 - 1.81: 32 Bond restraints: 9149 Sorted by residual: bond pdb=" C GLU A 370 " pdb=" O GLU A 370 " ideal model delta sigma weight residual 1.244 1.167 0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C LYS A 356 " pdb=" O LYS A 356 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.26e-02 6.30e+03 3.58e+01 bond pdb=" CA GLY A 413 " pdb=" C GLY A 413 " ideal model delta sigma weight residual 1.512 1.454 0.058 1.15e-02 7.56e+03 2.50e+01 bond pdb=" O3' G C 0 " pdb=" P A C 1 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.55e+01 bond pdb=" C LYS A 356 " pdb=" N LEU A 357 " ideal model delta sigma weight residual 1.334 1.279 0.056 1.43e-02 4.89e+03 1.51e+01 ... (remaining 9144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12606 2.01 - 4.02: 341 4.02 - 6.04: 55 6.04 - 8.05: 11 8.05 - 10.06: 6 Bond angle restraints: 13019 Sorted by residual: angle pdb=" N ARG A 334 " pdb=" CA ARG A 334 " pdb=" C ARG A 334 " ideal model delta sigma weight residual 113.16 103.10 10.06 1.24e+00 6.50e-01 6.58e+01 angle pdb=" N ASP A 156 " pdb=" CA ASP A 156 " pdb=" C ASP A 156 " ideal model delta sigma weight residual 111.14 104.53 6.61 1.08e+00 8.57e-01 3.75e+01 angle pdb=" N ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta sigma weight residual 110.57 118.62 -8.05 1.35e+00 5.49e-01 3.56e+01 angle pdb=" C THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta sigma weight residual 110.79 120.66 -9.87 1.66e+00 3.63e-01 3.54e+01 angle pdb=" O4' A C -11 " pdb=" C4' A C -11 " pdb=" C3' A C -11 " ideal model delta sigma weight residual 106.10 100.44 5.66 1.00e+00 1.00e+00 3.20e+01 ... (remaining 13014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 4658 21.21 - 42.42: 548 42.42 - 63.63: 257 63.63 - 84.84: 74 84.84 - 106.05: 9 Dihedral angle restraints: 5546 sinusoidal: 3475 harmonic: 2071 Sorted by residual: dihedral pdb=" C THR A 412 " pdb=" N THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta harmonic sigma weight residual -122.00 -137.57 15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta harmonic sigma weight residual 123.40 134.44 -11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" O4' U C-100 " pdb=" C1' U C-100 " pdb=" N1 U C-100 " pdb=" C2 U C-100 " ideal model delta sinusoidal sigma weight residual 232.00 167.57 64.43 1 1.70e+01 3.46e-03 1.89e+01 ... (remaining 5543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1444 0.098 - 0.196: 52 0.196 - 0.294: 5 0.294 - 0.392: 0 0.392 - 0.490: 3 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CA THR A 412 " pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CB THR A 412 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" C1' DT D -4 " pdb=" O4' DT D -4 " pdb=" C2' DT D -4 " pdb=" N1 DT D -4 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C1' DT D -5 " pdb=" O4' DT D -5 " pdb=" C2' DT D -5 " pdb=" N1 DT D -5 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 1501 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 731 " 0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C SER A 731 " -0.088 2.00e-02 2.50e+03 pdb=" O SER A 731 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA A 732 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 385 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLU A 385 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU A 385 " 0.026 2.00e-02 2.50e+03 pdb=" N THR A 386 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 684 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLN A 684 " 0.065 2.00e-02 2.50e+03 pdb=" O GLN A 684 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR A 685 " -0.023 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1391 2.75 - 3.29: 8245 3.29 - 3.83: 16412 3.83 - 4.36: 19783 4.36 - 4.90: 29550 Nonbonded interactions: 75381 Sorted by model distance: nonbonded pdb=" N ARG A 240 " pdb=" OP1 G C 6 " model vdw 2.219 3.120 nonbonded pdb=" O CYS A 91 " pdb=" OG SER A 92 " model vdw 2.221 3.040 nonbonded pdb=" OP1 DA B 23 " pdb=" NZ LYS A 488 " model vdw 2.236 3.120 nonbonded pdb=" O GLU A 440 " pdb=" O4 U C-101 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLN A 878 " pdb=" NZ LYS A 882 " model vdw 2.271 3.120 ... (remaining 75376 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.820 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:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 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 : 0.006 0.076 9149 Z= 0.333 Angle : 0.793 10.060 13019 Z= 0.494 Chirality : 0.047 0.490 1504 Planarity : 0.006 0.057 1162 Dihedral : 21.145 106.055 4214 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 0.71 % Allowed : 1.07 % Favored : 98.22 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % 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: -2.35 (0.31), residues: 713 helix: -0.72 (0.28), residues: 320 sheet: -1.56 (0.48), residues: 100 loop : -2.45 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 874 TYR 0.017 0.002 TYR A 241 PHE 0.036 0.002 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 9149) covalent geometry : angle 0.79278 (13019) hydrogen bonds : bond 0.12353 ( 392) hydrogen bonds : angle 6.36460 ( 1024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.240 Fit side-chains REVERT: A 22 GLN cc_start: 0.7509 (mt0) cc_final: 0.7156 (mm110) REVERT: A 90 LYS cc_start: 0.6715 (ptpt) cc_final: 0.6354 (pptt) REVERT: A 262 TYR cc_start: 0.8103 (t80) cc_final: 0.7790 (t80) REVERT: A 384 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6363 (mt-10) REVERT: A 390 LYS cc_start: 0.6322 (mmtt) cc_final: 0.5923 (tppt) REVERT: A 410 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5682 (tt0) REVERT: A 693 GLU cc_start: 0.7223 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 850 ARG cc_start: 0.6083 (mtt-85) cc_final: 0.4648 (mtt-85) REVERT: A 851 LYS cc_start: 0.6813 (tttp) cc_final: 0.6474 (tptp) outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 0.6697 time to fit residues: 76.0973 Evaluate side-chains 80 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 303 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.250043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.217374 restraints weight = 9538.810| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 2.00 r_work: 0.4011 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9149 Z= 0.177 Angle : 0.650 6.359 13019 Z= 0.338 Chirality : 0.037 0.167 1504 Planarity : 0.006 0.089 1162 Dihedral : 22.060 103.059 2845 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 3.02 % Allowed : 11.01 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.32), residues: 713 helix: 0.01 (0.29), residues: 318 sheet: -1.31 (0.51), residues: 98 loop : -2.11 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 687 TYR 0.019 0.002 TYR A 155 PHE 0.020 0.002 PHE A 717 TRP 0.017 0.002 TRP A 520 HIS 0.006 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9149) covalent geometry : angle 0.64992 (13019) hydrogen bonds : bond 0.04700 ( 392) hydrogen bonds : angle 4.90367 ( 1024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.152 Fit side-chains REVERT: A 22 GLN cc_start: 0.7382 (mt0) cc_final: 0.7029 (mm110) REVERT: A 90 LYS cc_start: 0.6696 (ptpt) cc_final: 0.6267 (pptt) REVERT: A 133 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7009 (mtt) REVERT: A 155 TYR cc_start: 0.7564 (t80) cc_final: 0.7084 (t80) REVERT: A 197 TYR cc_start: 0.6632 (t80) cc_final: 0.6232 (t80) REVERT: A 262 TYR cc_start: 0.8080 (t80) cc_final: 0.7814 (t80) REVERT: A 384 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6532 (mt-10) REVERT: A 390 LYS cc_start: 0.6441 (mmtt) cc_final: 0.5731 (ptmm) REVERT: A 410 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6353 (tt0) REVERT: A 489 LYS cc_start: 0.7964 (ptpp) cc_final: 0.7649 (pttt) REVERT: A 636 ARG cc_start: 0.6872 (mmt180) cc_final: 0.6565 (mmm-85) REVERT: A 683 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6378 (tpt) REVERT: A 693 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 698 GLU cc_start: 0.7432 (tt0) cc_final: 0.6879 (tt0) REVERT: A 850 ARG cc_start: 0.6116 (mtt-85) cc_final: 0.4946 (mtt-85) REVERT: A 851 LYS cc_start: 0.6681 (tttp) cc_final: 0.6370 (tptt) REVERT: A 855 ARG cc_start: 0.5487 (tpp-160) cc_final: 0.5276 (tpp-160) outliers start: 17 outliers final: 4 residues processed: 85 average time/residue: 0.6252 time to fit residues: 56.1682 Evaluate side-chains 80 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.251090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.218554 restraints weight = 9455.055| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.95 r_work: 0.4032 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9149 Z= 0.156 Angle : 0.604 6.377 13019 Z= 0.315 Chirality : 0.035 0.174 1504 Planarity : 0.005 0.082 1162 Dihedral : 21.925 101.417 2844 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.73 % Allowed : 13.85 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.32), residues: 713 helix: 0.23 (0.29), residues: 327 sheet: -1.32 (0.49), residues: 98 loop : -2.02 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 687 TYR 0.017 0.002 TYR A 241 PHE 0.020 0.002 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9149) covalent geometry : angle 0.60413 (13019) hydrogen bonds : bond 0.04270 ( 392) hydrogen bonds : angle 4.64120 ( 1024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.253 Fit side-chains REVERT: A 22 GLN cc_start: 0.7485 (mt0) cc_final: 0.7104 (mm110) REVERT: A 80 GLU cc_start: 0.6974 (tt0) cc_final: 0.6743 (tt0) REVERT: A 90 LYS cc_start: 0.6718 (ptpt) cc_final: 0.6228 (pptt) REVERT: A 93 MET cc_start: 0.6950 (mtm) cc_final: 0.6694 (mtm) REVERT: A 133 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: A 153 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7636 (ttpp) REVERT: A 155 TYR cc_start: 0.7575 (t80) cc_final: 0.7252 (t80) REVERT: A 197 TYR cc_start: 0.6823 (t80) cc_final: 0.6354 (t80) REVERT: A 262 TYR cc_start: 0.7953 (t80) cc_final: 0.7716 (t80) REVERT: A 303 GLN cc_start: 0.7889 (mt0) cc_final: 0.7656 (mt0) REVERT: A 384 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6632 (mt-10) REVERT: A 390 LYS cc_start: 0.6365 (mmtt) cc_final: 0.5946 (tppt) REVERT: A 410 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6387 (tt0) REVERT: A 489 LYS cc_start: 0.8006 (ptpp) cc_final: 0.7596 (pttp) REVERT: A 572 GLU cc_start: 0.7240 (mm-30) cc_final: 0.5879 (tp30) REVERT: A 636 ARG cc_start: 0.6847 (mmt180) cc_final: 0.6572 (mmm-85) REVERT: A 683 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6371 (tpt) REVERT: A 698 GLU cc_start: 0.7470 (tt0) cc_final: 0.6876 (tt0) REVERT: A 851 LYS cc_start: 0.6561 (tttp) cc_final: 0.6233 (tptt) outliers start: 21 outliers final: 7 residues processed: 98 average time/residue: 0.5300 time to fit residues: 55.0818 Evaluate side-chains 88 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4682 r_free = 0.4682 target = 0.249649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.216310 restraints weight = 9538.395| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 1.98 r_work: 0.4002 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9149 Z= 0.178 Angle : 0.627 8.309 13019 Z= 0.324 Chirality : 0.036 0.173 1504 Planarity : 0.005 0.088 1162 Dihedral : 21.903 101.322 2844 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 4.44 % Allowed : 14.03 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.32), residues: 713 helix: 0.24 (0.28), residues: 328 sheet: -1.20 (0.50), residues: 99 loop : -1.96 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 855 TYR 0.016 0.002 TYR A 725 PHE 0.019 0.002 PHE A 717 TRP 0.018 0.002 TRP A 520 HIS 0.005 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9149) covalent geometry : angle 0.62729 (13019) hydrogen bonds : bond 0.04393 ( 392) hydrogen bonds : angle 4.65343 ( 1024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.155 Fit side-chains REVERT: A 22 GLN cc_start: 0.7487 (mt0) cc_final: 0.7086 (mm110) REVERT: A 90 LYS cc_start: 0.6748 (ptpt) cc_final: 0.5638 (mmtp) REVERT: A 93 MET cc_start: 0.7021 (mtm) cc_final: 0.6793 (mtm) REVERT: A 133 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: A 153 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7684 (ttpp) REVERT: A 155 TYR cc_start: 0.7526 (t80) cc_final: 0.7230 (t80) REVERT: A 197 TYR cc_start: 0.6727 (t80) cc_final: 0.6365 (t80) REVERT: A 255 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6966 (pt0) REVERT: A 262 TYR cc_start: 0.7959 (t80) cc_final: 0.7689 (t80) REVERT: A 303 GLN cc_start: 0.7895 (mt0) cc_final: 0.7647 (mt0) REVERT: A 333 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7490 (mm) REVERT: A 390 LYS cc_start: 0.6451 (mmtt) cc_final: 0.5973 (tppt) REVERT: A 410 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6397 (tt0) REVERT: A 489 LYS cc_start: 0.8055 (ptpp) cc_final: 0.7632 (pttp) REVERT: A 572 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6238 (tp30) REVERT: A 683 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6408 (tpt) REVERT: A 698 GLU cc_start: 0.7423 (tt0) cc_final: 0.6905 (tt0) REVERT: A 851 LYS cc_start: 0.6652 (tttp) cc_final: 0.6328 (tptt) REVERT: A 855 ARG cc_start: 0.5336 (tpp-160) cc_final: 0.4616 (tmm160) outliers start: 25 outliers final: 9 residues processed: 93 average time/residue: 0.5294 time to fit residues: 52.2393 Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 410 GLN A 715 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.247909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.215736 restraints weight = 9477.573| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 1.92 r_work: 0.3973 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9149 Z= 0.197 Angle : 0.643 8.443 13019 Z= 0.333 Chirality : 0.037 0.177 1504 Planarity : 0.005 0.085 1162 Dihedral : 21.918 101.198 2844 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 4.97 % Allowed : 15.28 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.31), residues: 713 helix: 0.21 (0.29), residues: 327 sheet: -1.28 (0.48), residues: 109 loop : -2.08 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 687 TYR 0.016 0.002 TYR A 241 PHE 0.026 0.002 PHE A 717 TRP 0.019 0.002 TRP A 520 HIS 0.006 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9149) covalent geometry : angle 0.64332 (13019) hydrogen bonds : bond 0.04534 ( 392) hydrogen bonds : angle 4.71355 ( 1024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.156 Fit side-chains REVERT: A 22 GLN cc_start: 0.7484 (mt0) cc_final: 0.7133 (mm110) REVERT: A 90 LYS cc_start: 0.6781 (ptpt) cc_final: 0.5547 (mmtp) REVERT: A 93 MET cc_start: 0.7052 (mtm) cc_final: 0.6825 (mtm) REVERT: A 130 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 133 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6841 (mtt) REVERT: A 149 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6729 (pt0) REVERT: A 153 LYS cc_start: 0.7991 (tmmt) cc_final: 0.7672 (ttpp) REVERT: A 197 TYR cc_start: 0.6520 (t80) cc_final: 0.6209 (t80) REVERT: A 255 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7011 (pt0) REVERT: A 262 TYR cc_start: 0.8005 (t80) cc_final: 0.7746 (t80) REVERT: A 303 GLN cc_start: 0.7918 (mt0) cc_final: 0.7671 (mt0) REVERT: A 333 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7455 (mm) REVERT: A 390 LYS cc_start: 0.6461 (mmtt) cc_final: 0.5909 (tppt) REVERT: A 410 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: A 489 LYS cc_start: 0.8052 (ptpp) cc_final: 0.7639 (pttt) REVERT: A 500 LYS cc_start: 0.7256 (mtpp) cc_final: 0.6922 (pmmt) REVERT: A 572 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6263 (OUTLIER) REVERT: A 683 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6351 (tpt) REVERT: A 698 GLU cc_start: 0.7480 (tt0) cc_final: 0.6978 (tt0) REVERT: A 851 LYS cc_start: 0.6666 (tttp) cc_final: 0.6366 (tptt) REVERT: A 855 ARG cc_start: 0.5523 (tpp-160) cc_final: 0.5208 (tpp-160) outliers start: 28 outliers final: 11 residues processed: 96 average time/residue: 0.5393 time to fit residues: 54.9012 Evaluate side-chains 91 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.251598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.218846 restraints weight = 9542.888| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 1.94 r_work: 0.4007 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9149 Z= 0.139 Angle : 0.593 8.385 13019 Z= 0.309 Chirality : 0.034 0.268 1504 Planarity : 0.005 0.089 1162 Dihedral : 21.900 100.545 2844 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.73 % Allowed : 17.58 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.32), residues: 713 helix: 0.43 (0.29), residues: 327 sheet: -1.31 (0.52), residues: 100 loop : -1.97 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 687 TYR 0.017 0.001 TYR A 241 PHE 0.012 0.001 PHE A 717 TRP 0.016 0.002 TRP A 441 HIS 0.005 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9149) covalent geometry : angle 0.59300 (13019) hydrogen bonds : bond 0.04041 ( 392) hydrogen bonds : angle 4.46616 ( 1024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.258 Fit side-chains REVERT: A 22 GLN cc_start: 0.7429 (mt0) cc_final: 0.7077 (mm110) REVERT: A 90 LYS cc_start: 0.6809 (ptpt) cc_final: 0.5605 (mmtp) REVERT: A 133 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6952 (mtt) REVERT: A 197 TYR cc_start: 0.6488 (t80) cc_final: 0.6254 (t80) REVERT: A 255 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6960 (pt0) REVERT: A 262 TYR cc_start: 0.8003 (t80) cc_final: 0.7781 (t80) REVERT: A 303 GLN cc_start: 0.7886 (mt0) cc_final: 0.7644 (mt0) REVERT: A 390 LYS cc_start: 0.6458 (mmtt) cc_final: 0.5897 (tppt) REVERT: A 410 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6327 (tt0) REVERT: A 500 LYS cc_start: 0.7338 (mtpp) cc_final: 0.6971 (pmmt) REVERT: A 572 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6168 (tp30) REVERT: A 683 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6325 (tpt) REVERT: A 698 GLU cc_start: 0.7404 (tt0) cc_final: 0.6724 (tt0) REVERT: A 851 LYS cc_start: 0.6721 (tttp) cc_final: 0.6418 (tptt) REVERT: A 855 ARG cc_start: 0.5490 (tpp-160) cc_final: 0.5192 (tpp-160) outliers start: 21 outliers final: 8 residues processed: 90 average time/residue: 0.5348 time to fit residues: 51.2084 Evaluate side-chains 88 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 24 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.4706 r_free = 0.4706 target = 0.252701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.220507 restraints weight = 9555.725| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 1.93 r_work: 0.4047 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9149 Z= 0.138 Angle : 0.588 7.666 13019 Z= 0.307 Chirality : 0.034 0.171 1504 Planarity : 0.005 0.081 1162 Dihedral : 21.878 100.216 2844 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.20 % Allowed : 19.72 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.32), residues: 713 helix: 0.59 (0.29), residues: 327 sheet: -1.31 (0.51), residues: 101 loop : -1.90 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 687 TYR 0.017 0.001 TYR A 241 PHE 0.013 0.001 PHE A 717 TRP 0.013 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9149) covalent geometry : angle 0.58779 (13019) hydrogen bonds : bond 0.04031 ( 392) hydrogen bonds : angle 4.44306 ( 1024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.229 Fit side-chains REVERT: A 22 GLN cc_start: 0.7421 (mt0) cc_final: 0.7122 (mm110) REVERT: A 48 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7365 (mp) REVERT: A 90 LYS cc_start: 0.6731 (ptpt) cc_final: 0.5586 (mmtp) REVERT: A 133 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.7017 (mtt) REVERT: A 303 GLN cc_start: 0.7896 (mt0) cc_final: 0.7677 (mt0) REVERT: A 390 LYS cc_start: 0.6706 (mmtt) cc_final: 0.6147 (tppt) REVERT: A 410 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6406 (tt0) REVERT: A 500 LYS cc_start: 0.7164 (mtpp) cc_final: 0.6929 (pmmt) REVERT: A 572 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6323 (tp30) REVERT: A 636 ARG cc_start: 0.6936 (mmt180) cc_final: 0.6695 (mmm-85) REVERT: A 683 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6485 (tpt) REVERT: A 687 ARG cc_start: 0.6932 (mtp-110) cc_final: 0.5503 (ptm160) REVERT: A 698 GLU cc_start: 0.7306 (tt0) cc_final: 0.6548 (tt0) REVERT: A 851 LYS cc_start: 0.6820 (tttp) cc_final: 0.6515 (tptt) REVERT: A 855 ARG cc_start: 0.5753 (tpp-160) cc_final: 0.5505 (tpp-160) outliers start: 18 outliers final: 8 residues processed: 87 average time/residue: 0.5114 time to fit residues: 47.3166 Evaluate side-chains 84 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 74 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.251693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.219296 restraints weight = 9432.211| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.89 r_work: 0.4023 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9149 Z= 0.152 Angle : 0.599 7.684 13019 Z= 0.312 Chirality : 0.034 0.174 1504 Planarity : 0.005 0.081 1162 Dihedral : 21.862 99.827 2844 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.09 % Allowed : 19.01 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.32), residues: 713 helix: 0.64 (0.29), residues: 327 sheet: -1.32 (0.52), residues: 100 loop : -1.89 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 687 TYR 0.017 0.001 TYR A 241 PHE 0.013 0.001 PHE A 717 TRP 0.017 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9149) covalent geometry : angle 0.59917 (13019) hydrogen bonds : bond 0.04075 ( 392) hydrogen bonds : angle 4.45582 ( 1024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.151 Fit side-chains REVERT: A 22 GLN cc_start: 0.7414 (mt0) cc_final: 0.7214 (mm110) REVERT: A 90 LYS cc_start: 0.6584 (ptpt) cc_final: 0.5456 (mmtp) REVERT: A 133 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6922 (mtt) REVERT: A 255 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6968 (pt0) REVERT: A 303 GLN cc_start: 0.8018 (mt0) cc_final: 0.7797 (mt0) REVERT: A 390 LYS cc_start: 0.6768 (mmtt) cc_final: 0.6341 (tppt) REVERT: A 410 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6507 (tt0) REVERT: A 500 LYS cc_start: 0.7174 (mtpp) cc_final: 0.6900 (pmmt) REVERT: A 572 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6313 (tp30) REVERT: A 683 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6429 (tpt) REVERT: A 698 GLU cc_start: 0.7434 (tt0) cc_final: 0.6795 (tt0) REVERT: A 851 LYS cc_start: 0.6933 (tttp) cc_final: 0.6634 (tptt) REVERT: A 855 ARG cc_start: 0.5884 (tpp-160) cc_final: 0.5641 (tpp-160) outliers start: 23 outliers final: 12 residues processed: 87 average time/residue: 0.5357 time to fit residues: 49.4174 Evaluate side-chains 89 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.251179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.211305 restraints weight = 9447.432| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.16 r_work: 0.3992 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9149 Z= 0.161 Angle : 0.612 9.392 13019 Z= 0.317 Chirality : 0.034 0.169 1504 Planarity : 0.005 0.077 1162 Dihedral : 21.865 99.611 2844 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.55 % Allowed : 20.25 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.32), residues: 713 helix: 0.58 (0.29), residues: 329 sheet: -1.33 (0.51), residues: 100 loop : -1.88 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 687 TYR 0.017 0.001 TYR A 241 PHE 0.013 0.001 PHE A 717 TRP 0.017 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9149) covalent geometry : angle 0.61203 (13019) hydrogen bonds : bond 0.04099 ( 392) hydrogen bonds : angle 4.47934 ( 1024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.226 Fit side-chains REVERT: A 22 GLN cc_start: 0.7430 (mt0) cc_final: 0.7158 (mm110) REVERT: A 90 LYS cc_start: 0.6686 (ptpt) cc_final: 0.5514 (mmtm) REVERT: A 133 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6826 (mtt) REVERT: A 255 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6806 (pt0) REVERT: A 303 GLN cc_start: 0.7977 (mt0) cc_final: 0.7727 (mt0) REVERT: A 390 LYS cc_start: 0.6592 (mmtt) cc_final: 0.6232 (tppt) REVERT: A 410 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: A 500 LYS cc_start: 0.7178 (mtpp) cc_final: 0.6849 (pmmt) REVERT: A 572 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6206 (OUTLIER) REVERT: A 636 ARG cc_start: 0.6902 (mmt180) cc_final: 0.6587 (mmm-85) REVERT: A 683 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6210 (tpt) REVERT: A 698 GLU cc_start: 0.7423 (tt0) cc_final: 0.6699 (tt0) REVERT: A 851 LYS cc_start: 0.6784 (tttp) cc_final: 0.6476 (tptt) REVERT: A 855 ARG cc_start: 0.5627 (tpp-160) cc_final: 0.5326 (tpp-160) outliers start: 20 outliers final: 13 residues processed: 81 average time/residue: 0.5736 time to fit residues: 49.4095 Evaluate side-chains 87 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.250477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.217093 restraints weight = 9427.664| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 1.96 r_work: 0.4003 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9149 Z= 0.170 Angle : 0.619 8.616 13019 Z= 0.321 Chirality : 0.035 0.166 1504 Planarity : 0.005 0.078 1162 Dihedral : 21.875 99.477 2844 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.02 % Allowed : 20.96 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.32), residues: 713 helix: 0.58 (0.29), residues: 326 sheet: -1.42 (0.50), residues: 102 loop : -1.98 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 687 TYR 0.017 0.002 TYR A 241 PHE 0.014 0.002 PHE A 717 TRP 0.018 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9149) covalent geometry : angle 0.61935 (13019) hydrogen bonds : bond 0.04199 ( 392) hydrogen bonds : angle 4.50391 ( 1024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.180 Fit side-chains REVERT: A 22 GLN cc_start: 0.7409 (mt0) cc_final: 0.7201 (mm110) REVERT: A 90 LYS cc_start: 0.6605 (ptpt) cc_final: 0.5527 (mmtm) REVERT: A 133 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6983 (mtt) REVERT: A 255 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7027 (pt0) REVERT: A 303 GLN cc_start: 0.8013 (mt0) cc_final: 0.7796 (mt0) REVERT: A 326 GLU cc_start: 0.6257 (tm-30) cc_final: 0.5418 (mt-10) REVERT: A 390 LYS cc_start: 0.6739 (mmtt) cc_final: 0.6393 (tppt) REVERT: A 410 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6630 (tt0) REVERT: A 500 LYS cc_start: 0.7186 (mtpp) cc_final: 0.6922 (pmmt) REVERT: A 636 ARG cc_start: 0.6997 (mmt180) cc_final: 0.6707 (mmm-85) REVERT: A 683 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6288 (tpt) REVERT: A 698 GLU cc_start: 0.7528 (tt0) cc_final: 0.6938 (tt0) REVERT: A 851 LYS cc_start: 0.6973 (tttp) cc_final: 0.6679 (tptt) REVERT: A 855 ARG cc_start: 0.5938 (tpp-160) cc_final: 0.5677 (tpp-160) outliers start: 17 outliers final: 10 residues processed: 76 average time/residue: 0.5584 time to fit residues: 44.9059 Evaluate side-chains 82 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 0.0870 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.251377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.217732 restraints weight = 9417.818| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 2.01 r_work: 0.4011 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9149 Z= 0.153 Angle : 0.604 8.888 13019 Z= 0.314 Chirality : 0.034 0.168 1504 Planarity : 0.005 0.071 1162 Dihedral : 21.875 99.085 2844 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.49 % Allowed : 22.20 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.32), residues: 713 helix: 0.63 (0.29), residues: 326 sheet: -1.41 (0.50), residues: 102 loop : -1.95 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 687 TYR 0.018 0.002 TYR A 241 PHE 0.011 0.001 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9149) covalent geometry : angle 0.60417 (13019) hydrogen bonds : bond 0.04049 ( 392) hydrogen bonds : angle 4.43598 ( 1024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.58 seconds wall clock time: 40 minutes 18.38 seconds (2418.38 seconds total)