Starting phenix.real_space_refine on Wed Sep 17 08:01:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9l_39082/09_2025/8y9l_39082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9l_39082/09_2025/8y9l_39082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9l_39082/09_2025/8y9l_39082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9l_39082/09_2025/8y9l_39082.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9l_39082/09_2025/8y9l_39082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9l_39082/09_2025/8y9l_39082.cif" } resolution = 3.0 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= 0.000 sd= 0.077 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 4299 2.51 5 N 1241 2.21 5 O 1401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7008 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6127 Classifications: {'peptide': 757} Link IDs: {'PTRANS': 26, 'TRANS': 730} Chain breaks: 5 Chain: "B" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 880 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 4, 'rna3p': 36} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.24 Number of scatterers: 7008 At special positions: 0 Unit cell: (86.355, 98.325, 101.745, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 41 15.00 Mg 1 11.99 O 1401 8.00 N 1241 7.00 C 4299 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: 0.54 Conformation dependent library (CDL) restraints added in 331.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 47.0% alpha, 12.3% beta 8 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 3.667A pdb=" N TRP A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.976A pdb=" N ASP A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 53 " --> pdb=" O ARG A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 59 through 72 Processing helix chain 'A' and resid 74 through 88 removed outlier: 3.588A pdb=" N ALA A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.801A pdb=" N SER A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.776A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 230 removed outlier: 3.594A pdb=" N HIS A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.913A pdb=" N LEU A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.687A pdb=" N LEU A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 314 removed outlier: 3.764A pdb=" N LYS A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.627A pdb=" N ILE A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 512 through 537 removed outlier: 3.925A pdb=" N SER A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 550 Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.786A pdb=" N GLN A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 610 removed outlier: 3.773A pdb=" N LEU A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 649 removed outlier: 3.801A pdb=" N TYR A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.584A pdb=" N LEU A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 831 through 847 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 4.584A pdb=" N SER A 429 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU A 404 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 332 removed outlier: 4.919A pdb=" N PHE A 420 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE A 359 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR A 17 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS A 357 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 349 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 342 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 489 removed outlier: 4.064A pdb=" N TYR A 494 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A 460 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N PHE A 656 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY A 462 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N GLU A 658 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AA5, first strand: chain 'A' and resid 760 through 761 removed outlier: 3.569A pdb=" N GLU A 827 " --> pdb=" O HIS A 824 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 796 through 800 removed outlier: 3.747A pdb=" N ARG A 796 " --> pdb=" O THR A 808 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1042 1.27 - 1.41: 1928 1.41 - 1.54: 4114 1.54 - 1.68: 115 1.68 - 1.81: 39 Bond restraints: 7238 Sorted by residual: bond pdb=" C PRO A 7 " pdb=" O PRO A 7 " ideal model delta sigma weight residual 1.233 1.135 0.098 1.13e-02 7.83e+03 7.52e+01 bond pdb=" O3' C B 0 " pdb=" P A B 1 " ideal model delta sigma weight residual 1.607 1.515 0.092 1.50e-02 4.44e+03 3.78e+01 bond pdb=" O3' U B 2 " pdb=" P A B 3 " ideal model delta sigma weight residual 1.607 1.523 0.084 1.50e-02 4.44e+03 3.17e+01 bond pdb=" P U B 2 " pdb=" OP2 U B 2 " ideal model delta sigma weight residual 1.485 1.376 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" P U B 2 " pdb=" OP1 U B 2 " ideal model delta sigma weight residual 1.485 1.380 0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 7233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 9890 4.33 - 8.65: 50 8.65 - 12.98: 7 12.98 - 17.31: 3 17.31 - 21.64: 2 Bond angle restraints: 9952 Sorted by residual: angle pdb=" CA ILE A 6 " pdb=" C ILE A 6 " pdb=" O ILE A 6 " ideal model delta sigma weight residual 119.15 111.19 7.96 5.90e-01 2.87e+00 1.82e+02 angle pdb=" C PRO A 7 " pdb=" CA PRO A 7 " pdb=" CB PRO A 7 " ideal model delta sigma weight residual 111.46 97.82 13.64 1.21e+00 6.83e-01 1.27e+02 angle pdb=" O2' A B 3 " pdb=" C2' A B 3 " pdb=" C1' A B 3 " ideal model delta sigma weight residual 108.40 122.29 -13.89 1.50e+00 4.44e-01 8.57e+01 angle pdb=" CA ILE A 6 " pdb=" C ILE A 6 " pdb=" N PRO A 7 " ideal model delta sigma weight residual 119.22 125.85 -6.63 7.80e-01 1.64e+00 7.23e+01 angle pdb=" C4' A B 1 " pdb=" C3' A B 1 " pdb=" O3' A B 1 " ideal model delta sigma weight residual 109.40 122.07 -12.67 1.50e+00 4.44e-01 7.14e+01 ... (remaining 9947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.02: 4137 29.02 - 58.05: 232 58.05 - 87.07: 61 87.07 - 116.10: 2 116.10 - 145.12: 1 Dihedral angle restraints: 4433 sinusoidal: 2229 harmonic: 2204 Sorted by residual: dihedral pdb=" O4' U B -18 " pdb=" C1' U B -18 " pdb=" N1 U B -18 " pdb=" C2 U B -18 " ideal model delta sinusoidal sigma weight residual 200.00 54.88 145.12 1 1.50e+01 4.44e-03 7.77e+01 dihedral pdb=" O4' U B 5 " pdb=" C1' U B 5 " pdb=" N1 U B 5 " pdb=" C2 U B 5 " ideal model delta sinusoidal sigma weight residual -128.00 -23.43 -104.57 1 1.70e+01 3.46e-03 4.16e+01 dihedral pdb=" C3' U B 5 " pdb=" C4' U B 5 " pdb=" O4' U B 5 " pdb=" C1' U B 5 " ideal model delta sinusoidal sigma weight residual -2.00 40.96 -42.96 1 8.00e+00 1.56e-02 4.02e+01 ... (remaining 4430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 1099 0.208 - 0.417: 12 0.417 - 0.625: 2 0.625 - 0.833: 0 0.833 - 1.041: 1 Chirality restraints: 1114 Sorted by residual: chirality pdb=" C2' A B 3 " pdb=" C3' A B 3 " pdb=" O2' A B 3 " pdb=" C1' A B 3 " both_signs ideal model delta sigma weight residual False -2.75 -1.71 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" CA ILE A 6 " pdb=" N ILE A 6 " pdb=" C ILE A 6 " pdb=" CB ILE A 6 " both_signs ideal model delta sigma weight residual False 2.43 2.96 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -1.89 0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 1111 not shown) Planarity restraints: 1115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 838 " -0.029 2.00e-02 2.50e+03 5.95e-02 3.54e+01 pdb=" C LYS A 838 " 0.103 2.00e-02 2.50e+03 pdb=" O LYS A 838 " -0.039 2.00e-02 2.50e+03 pdb=" N ASP A 839 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 852 " -0.430 9.50e-02 1.11e+02 1.93e-01 2.28e+01 pdb=" NE ARG A 852 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 852 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 852 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 852 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 853 " -0.330 9.50e-02 1.11e+02 1.48e-01 1.35e+01 pdb=" NE ARG A 853 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 853 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 853 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 853 " -0.013 2.00e-02 2.50e+03 ... (remaining 1112 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 48 2.54 - 3.13: 5128 3.13 - 3.72: 10538 3.72 - 4.31: 15108 4.31 - 4.90: 24814 Nonbonded interactions: 55636 Sorted by model distance: nonbonded pdb=" O2' C B 0 " pdb=" OP1 U B 2 " model vdw 1.953 3.040 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A 901 " model vdw 2.114 2.170 nonbonded pdb=" ND1 HIS A 4 " pdb=" O HIS A 430 " model vdw 2.175 3.120 nonbonded pdb=" OD2 ASP A 31 " pdb=" OH TYR A 195 " model vdw 2.185 3.040 nonbonded pdb=" ND2 ASN A 753 " pdb=" O PHE A 867 " model vdw 2.216 3.120 ... (remaining 55631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.320 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 0.109 7238 Z= 0.344 Angle : 0.903 21.637 9952 Z= 0.555 Chirality : 0.065 1.041 1114 Planarity : 0.009 0.193 1115 Dihedral : 17.888 145.122 3015 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.11 % Rotamer: Outliers : 1.52 % Allowed : 0.91 % Favored : 97.57 % Cbeta Deviations : 0.42 % 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: -0.24 (0.30), residues: 745 helix: 0.37 (0.28), residues: 352 sheet: 0.03 (0.47), residues: 124 loop : -0.81 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 852 TYR 0.014 0.001 TYR A 214 PHE 0.026 0.002 PHE A 785 TRP 0.027 0.002 TRP A 323 HIS 0.012 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 7238) covalent geometry : angle 0.90284 ( 9952) hydrogen bonds : bond 0.19183 ( 315) hydrogen bonds : angle 7.30116 ( 880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.251 Fit side-chains REVERT: A 53 ASP cc_start: 0.7148 (m-30) cc_final: 0.6920 (t70) REVERT: A 186 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7819 (pttp) REVERT: A 295 TRP cc_start: 0.6543 (t60) cc_final: 0.6342 (t60) REVERT: A 399 ILE cc_start: 0.8192 (mp) cc_final: 0.7992 (mt) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 0.4987 time to fit residues: 46.6033 Evaluate side-chains 63 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PRO Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 853 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 276 GLN A 603 ASN A 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.193093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165056 restraints weight = 8205.701| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.64 r_work: 0.3753 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7238 Z= 0.138 Angle : 0.547 6.786 9952 Z= 0.285 Chirality : 0.041 0.349 1114 Planarity : 0.004 0.046 1115 Dihedral : 17.773 145.652 1500 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.21 % Allowed : 7.89 % Favored : 90.90 % 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: 0.29 (0.31), residues: 745 helix: 0.89 (0.28), residues: 353 sheet: 0.09 (0.49), residues: 118 loop : -0.57 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 630 TYR 0.013 0.001 TYR A 214 PHE 0.008 0.001 PHE A 531 TRP 0.024 0.002 TRP A 323 HIS 0.004 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7238) covalent geometry : angle 0.54728 ( 9952) hydrogen bonds : bond 0.05128 ( 315) hydrogen bonds : angle 4.88967 ( 880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.257 Fit side-chains REVERT: A 17 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7880 (p90) REVERT: A 53 ASP cc_start: 0.7639 (m-30) cc_final: 0.6703 (t70) REVERT: A 186 LYS cc_start: 0.8298 (ptmm) cc_final: 0.8024 (pttp) REVERT: A 295 TRP cc_start: 0.6074 (t60) cc_final: 0.5827 (t60) REVERT: A 377 ARG cc_start: 0.7486 (ptt90) cc_final: 0.7045 (ptt-90) outliers start: 8 outliers final: 2 residues processed: 72 average time/residue: 0.4258 time to fit residues: 32.9430 Evaluate side-chains 59 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 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 753 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.183739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154107 restraints weight = 8518.744| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.88 r_work: 0.3574 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7238 Z= 0.272 Angle : 0.670 7.586 9952 Z= 0.345 Chirality : 0.045 0.300 1114 Planarity : 0.005 0.047 1115 Dihedral : 17.909 145.482 1484 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.88 % Allowed : 9.41 % Favored : 87.71 % 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: -0.18 (0.30), residues: 745 helix: 0.44 (0.27), residues: 357 sheet: -0.25 (0.46), residues: 128 loop : -0.64 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 820 TYR 0.022 0.002 TYR A 214 PHE 0.011 0.002 PHE A 420 TRP 0.024 0.002 TRP A 323 HIS 0.008 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 7238) covalent geometry : angle 0.67014 ( 9952) hydrogen bonds : bond 0.06714 ( 315) hydrogen bonds : angle 4.98756 ( 880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.248 Fit side-chains REVERT: A 17 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7558 (p90) REVERT: A 186 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8265 (pttp) REVERT: A 295 TRP cc_start: 0.6095 (t60) cc_final: 0.5843 (t60) REVERT: A 377 ARG cc_start: 0.7478 (ptt90) cc_final: 0.7017 (ptt-90) REVERT: A 391 ARG cc_start: 0.8568 (mmt180) cc_final: 0.8326 (tpm170) outliers start: 19 outliers final: 6 residues processed: 70 average time/residue: 0.4618 time to fit residues: 34.6361 Evaluate side-chains 63 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 763 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.187536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158016 restraints weight = 8576.043| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.98 r_work: 0.3612 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7238 Z= 0.109 Angle : 0.498 6.571 9952 Z= 0.259 Chirality : 0.039 0.285 1114 Planarity : 0.004 0.045 1115 Dihedral : 17.695 144.027 1484 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.06 % Allowed : 14.42 % Favored : 84.52 % 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: 0.42 (0.31), residues: 745 helix: 1.12 (0.28), residues: 353 sheet: -0.01 (0.47), residues: 119 loop : -0.59 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.011 0.001 TYR A 214 PHE 0.006 0.001 PHE A 339 TRP 0.024 0.002 TRP A 323 HIS 0.006 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7238) covalent geometry : angle 0.49808 ( 9952) hydrogen bonds : bond 0.04253 ( 315) hydrogen bonds : angle 4.34905 ( 880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.390 Fit side-chains REVERT: A 17 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7552 (p90) REVERT: A 186 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8303 (pttp) REVERT: A 232 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8029 (mp) REVERT: A 357 LYS cc_start: 0.7261 (ptpp) cc_final: 0.6910 (ptpt) REVERT: A 377 ARG cc_start: 0.7390 (ptt90) cc_final: 0.6855 (ptt-90) REVERT: A 795 VAL cc_start: 0.8435 (p) cc_final: 0.8227 (m) REVERT: A 866 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8699 (m) outliers start: 7 outliers final: 2 residues processed: 68 average time/residue: 0.4234 time to fit residues: 31.2150 Evaluate side-chains 63 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 0.0970 chunk 48 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.184226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154142 restraints weight = 8616.260| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.00 r_work: 0.3544 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7238 Z= 0.195 Angle : 0.597 13.883 9952 Z= 0.300 Chirality : 0.041 0.211 1114 Planarity : 0.004 0.045 1115 Dihedral : 17.852 143.778 1484 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.82 % Allowed : 14.57 % Favored : 83.61 % 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: 0.24 (0.30), residues: 745 helix: 0.95 (0.28), residues: 353 sheet: -0.11 (0.47), residues: 119 loop : -0.64 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 820 TYR 0.023 0.002 TYR A 648 PHE 0.008 0.002 PHE A 242 TRP 0.026 0.002 TRP A 323 HIS 0.009 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 7238) covalent geometry : angle 0.59744 ( 9952) hydrogen bonds : bond 0.05718 ( 315) hydrogen bonds : angle 4.52462 ( 880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.214 Fit side-chains REVERT: A 17 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7586 (p90) REVERT: A 186 LYS cc_start: 0.8551 (ptmm) cc_final: 0.8322 (pttp) REVERT: A 232 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8117 (mp) REVERT: A 357 LYS cc_start: 0.7429 (ptpp) cc_final: 0.7056 (ptpt) REVERT: A 377 ARG cc_start: 0.7389 (ptt90) cc_final: 0.6871 (ptt-90) REVERT: A 391 ARG cc_start: 0.8596 (mmt180) cc_final: 0.8379 (tpp-160) REVERT: A 725 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6838 (mp0) REVERT: A 795 VAL cc_start: 0.8476 (p) cc_final: 0.8255 (m) REVERT: A 866 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8652 (m) outliers start: 12 outliers final: 3 residues processed: 74 average time/residue: 0.5239 time to fit residues: 41.1394 Evaluate side-chains 69 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.183315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153730 restraints weight = 8580.686| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.96 r_work: 0.3548 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7238 Z= 0.176 Angle : 0.576 13.298 9952 Z= 0.289 Chirality : 0.041 0.187 1114 Planarity : 0.004 0.045 1115 Dihedral : 17.870 142.517 1484 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.97 % Allowed : 15.33 % Favored : 82.70 % 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: 0.25 (0.30), residues: 745 helix: 0.96 (0.28), residues: 353 sheet: -0.11 (0.48), residues: 119 loop : -0.65 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 283 TYR 0.017 0.001 TYR A 648 PHE 0.008 0.001 PHE A 420 TRP 0.030 0.002 TRP A 323 HIS 0.009 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7238) covalent geometry : angle 0.57644 ( 9952) hydrogen bonds : bond 0.05326 ( 315) hydrogen bonds : angle 4.44622 ( 880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.257 Fit side-chains REVERT: A 17 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7535 (p90) REVERT: A 186 LYS cc_start: 0.8575 (ptmm) cc_final: 0.8353 (pttp) REVERT: A 232 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 357 LYS cc_start: 0.7416 (ptpp) cc_final: 0.7049 (ptpt) REVERT: A 377 ARG cc_start: 0.7429 (ptt90) cc_final: 0.6933 (ptt-90) REVERT: A 391 ARG cc_start: 0.8538 (mmt180) cc_final: 0.8314 (tpp-160) REVERT: A 725 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6844 (mp0) REVERT: A 866 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8690 (m) outliers start: 13 outliers final: 6 residues processed: 76 average time/residue: 0.5254 time to fit residues: 42.4572 Evaluate side-chains 71 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 19 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.184984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156045 restraints weight = 8456.261| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.93 r_work: 0.3582 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7238 Z= 0.127 Angle : 0.533 12.033 9952 Z= 0.266 Chirality : 0.039 0.189 1114 Planarity : 0.004 0.044 1115 Dihedral : 17.755 141.649 1484 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.82 % Allowed : 15.48 % Favored : 82.70 % 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: 0.47 (0.31), residues: 745 helix: 1.19 (0.28), residues: 352 sheet: -0.03 (0.48), residues: 119 loop : -0.59 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 680 TYR 0.015 0.001 TYR A 648 PHE 0.006 0.001 PHE A 339 TRP 0.032 0.002 TRP A 323 HIS 0.008 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7238) covalent geometry : angle 0.53284 ( 9952) hydrogen bonds : bond 0.04569 ( 315) hydrogen bonds : angle 4.28796 ( 880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.171 Fit side-chains REVERT: A 17 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7514 (p90) REVERT: A 186 LYS cc_start: 0.8570 (ptmm) cc_final: 0.8361 (pttp) REVERT: A 357 LYS cc_start: 0.7357 (ptpp) cc_final: 0.6994 (ptpt) REVERT: A 377 ARG cc_start: 0.7414 (ptt90) cc_final: 0.6939 (ptt-90) REVERT: A 391 ARG cc_start: 0.8536 (mmt180) cc_final: 0.8304 (tpp-160) REVERT: A 725 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6741 (mm-30) REVERT: A 795 VAL cc_start: 0.8489 (p) cc_final: 0.8280 (m) REVERT: A 866 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8690 (m) outliers start: 12 outliers final: 4 residues processed: 71 average time/residue: 0.5217 time to fit residues: 39.4681 Evaluate side-chains 68 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.180543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150738 restraints weight = 8676.809| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.97 r_work: 0.3515 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7238 Z= 0.230 Angle : 0.626 10.859 9952 Z= 0.316 Chirality : 0.043 0.184 1114 Planarity : 0.004 0.045 1115 Dihedral : 17.950 140.681 1484 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.67 % Allowed : 16.08 % Favored : 82.25 % 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: 0.06 (0.30), residues: 745 helix: 0.79 (0.27), residues: 352 sheet: -0.20 (0.48), residues: 119 loop : -0.71 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.020 0.002 TYR A 214 PHE 0.010 0.002 PHE A 420 TRP 0.044 0.003 TRP A 323 HIS 0.009 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 7238) covalent geometry : angle 0.62597 ( 9952) hydrogen bonds : bond 0.06125 ( 315) hydrogen bonds : angle 4.59526 ( 880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.167 Fit side-chains REVERT: A 17 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7443 (p90) REVERT: A 186 LYS cc_start: 0.8572 (ptmm) cc_final: 0.8269 (pttp) REVERT: A 290 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5836 (mp) REVERT: A 357 LYS cc_start: 0.7437 (ptpp) cc_final: 0.7139 (ptpt) REVERT: A 377 ARG cc_start: 0.7449 (ptt90) cc_final: 0.6950 (ptt-90) REVERT: A 391 ARG cc_start: 0.8555 (mmt180) cc_final: 0.8276 (tpm170) REVERT: A 446 LYS cc_start: 0.7881 (mmpt) cc_final: 0.7498 (tptt) REVERT: A 725 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6823 (mp0) REVERT: A 866 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8664 (m) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.5751 time to fit residues: 42.6051 Evaluate side-chains 69 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.185409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155816 restraints weight = 8437.026| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.03 r_work: 0.3579 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7238 Z= 0.110 Angle : 0.518 8.442 9952 Z= 0.262 Chirality : 0.039 0.227 1114 Planarity : 0.004 0.044 1115 Dihedral : 17.717 138.990 1484 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.06 % Allowed : 16.39 % Favored : 82.55 % 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: 0.50 (0.31), residues: 745 helix: 1.23 (0.28), residues: 352 sheet: -0.03 (0.48), residues: 119 loop : -0.58 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 680 TYR 0.012 0.001 TYR A 648 PHE 0.006 0.001 PHE A 35 TRP 0.070 0.003 TRP A 323 HIS 0.007 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7238) covalent geometry : angle 0.51831 ( 9952) hydrogen bonds : bond 0.04168 ( 315) hydrogen bonds : angle 4.22421 ( 880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.294 Fit side-chains REVERT: A 17 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7405 (p90) REVERT: A 186 LYS cc_start: 0.8565 (ptmm) cc_final: 0.8351 (pttp) REVERT: A 357 LYS cc_start: 0.7305 (ptpp) cc_final: 0.6936 (ptpt) REVERT: A 377 ARG cc_start: 0.7353 (ptt90) cc_final: 0.7081 (ptt-90) REVERT: A 391 ARG cc_start: 0.8523 (mmt180) cc_final: 0.8273 (tpp-160) REVERT: A 446 LYS cc_start: 0.7820 (mmpt) cc_final: 0.7405 (tptt) REVERT: A 725 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6747 (mm-30) REVERT: A 795 VAL cc_start: 0.8433 (p) cc_final: 0.8218 (m) REVERT: A 866 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (m) outliers start: 7 outliers final: 2 residues processed: 72 average time/residue: 0.5443 time to fit residues: 41.6254 Evaluate side-chains 69 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.176370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146535 restraints weight = 8571.880| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.05 r_work: 0.3477 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 7238 Z= 0.321 Angle : 0.721 9.465 9952 Z= 0.365 Chirality : 0.047 0.197 1114 Planarity : 0.005 0.045 1115 Dihedral : 18.041 138.553 1484 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.76 % Allowed : 16.84 % Favored : 82.40 % 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: -0.18 (0.30), residues: 745 helix: 0.56 (0.27), residues: 352 sheet: -0.29 (0.49), residues: 119 loop : -0.78 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 32 TYR 0.026 0.002 TYR A 214 PHE 0.013 0.002 PHE A 420 TRP 0.117 0.005 TRP A 323 HIS 0.012 0.002 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00748 ( 7238) covalent geometry : angle 0.72092 ( 9952) hydrogen bonds : bond 0.06989 ( 315) hydrogen bonds : angle 4.80229 ( 880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.267 Fit side-chains REVERT: A 17 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7458 (p90) REVERT: A 186 LYS cc_start: 0.8550 (ptmm) cc_final: 0.8236 (pttp) REVERT: A 197 LYS cc_start: 0.7185 (mttt) cc_final: 0.6963 (ttpt) REVERT: A 377 ARG cc_start: 0.7418 (ptt90) cc_final: 0.6898 (ptt-90) REVERT: A 391 ARG cc_start: 0.8570 (mmt180) cc_final: 0.8255 (tpm170) REVERT: A 446 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7312 (mptt) REVERT: A 725 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6811 (mp0) REVERT: A 866 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8622 (m) outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.5525 time to fit residues: 38.0268 Evaluate side-chains 68 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain A residue 866 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.184184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154817 restraints weight = 8481.791| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.96 r_work: 0.3582 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7238 Z= 0.118 Angle : 0.535 8.130 9952 Z= 0.272 Chirality : 0.040 0.244 1114 Planarity : 0.004 0.044 1115 Dihedral : 17.776 136.735 1484 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.76 % Allowed : 17.30 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.39 (0.31), residues: 745 helix: 1.13 (0.28), residues: 351 sheet: -0.12 (0.49), residues: 119 loop : -0.60 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.012 0.001 TYR A 648 PHE 0.008 0.001 PHE A 35 TRP 0.094 0.003 TRP A 323 HIS 0.006 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7238) covalent geometry : angle 0.53524 ( 9952) hydrogen bonds : bond 0.04413 ( 315) hydrogen bonds : angle 4.28714 ( 880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.02 seconds wall clock time: 40 minutes 45.85 seconds (2445.85 seconds total)