Starting phenix.real_space_refine on Wed Mar 4 18:19:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yap_72733/03_2026/9yap_72733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yap_72733/03_2026/9yap_72733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yap_72733/03_2026/9yap_72733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yap_72733/03_2026/9yap_72733.map" model { file = "/net/cci-nas-00/data/ceres_data/9yap_72733/03_2026/9yap_72733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yap_72733/03_2026/9yap_72733.cif" } resolution = 4.5 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= 0.004 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 S 51 5.16 5 C 5657 2.51 5 N 1554 2.21 5 O 1705 1.98 5 H 5934 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14901 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 11881 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 46, 'TRANS': 694} Chain breaks: 3 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Time building chain proxies: 2.38, per 1000 atoms: 0.16 Number of scatterers: 14901 At special positions: 0 Unit cell: (81.389, 102.41, 131.516, 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 51 16.00 O 1705 8.00 N 1554 7.00 C 5657 6.00 H 5934 1.00 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: 0.88 Conformation dependent library (CDL) restraints added in 432.2 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 14 sheets defined 30.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.528A pdb=" N GLN A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.875A pdb=" N ILE A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.536A pdb=" N LEU A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.684A pdb=" N LEU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 309 through 314' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.510A pdb=" N TYR A 326 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 removed outlier: 3.982A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.892A pdb=" N ALA A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 434 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.971A pdb=" N SER A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 621 through 632 Processing helix chain 'A' and resid 632 through 641 Processing helix chain 'A' and resid 661 through 668 removed outlier: 4.201A pdb=" N VAL A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 removed outlier: 3.797A pdb=" N VAL A 689 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 690 " --> pdb=" O ASN A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 754 through 758 removed outlier: 3.864A pdb=" N THR A 758 " --> pdb=" O PRO A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 869 through 878 Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.674A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65 removed outlier: 4.112A pdb=" N THR A 55 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR A 42 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 344 removed outlier: 7.493A pdb=" N GLY A 343 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 736 removed outlier: 7.093A pdb=" N LEU A 839 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLY A 735 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA A 837 " --> pdb=" O GLY A 735 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 821 " --> pdb=" O ILE A 840 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 745 through 752 removed outlier: 3.677A pdb=" N GLY A 807 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLU A 800 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE A 805 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.142A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP B 339 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 112 removed outlier: 6.108A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.520A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 Processing sheet with id=AB3, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.636A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5929 1.03 - 1.23: 8 1.23 - 1.42: 3796 1.42 - 1.62: 5265 1.62 - 1.81: 82 Bond restraints: 15080 Sorted by residual: bond pdb=" C VAL A 756 " pdb=" N ASP A 757 " ideal model delta sigma weight residual 1.333 1.319 0.014 1.41e-02 5.03e+03 1.02e+00 bond pdb=" CA ASN A 675 " pdb=" CB ASN A 675 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 7.78e-01 bond pdb=" CA VAL B 315 " pdb=" CB VAL B 315 " ideal model delta sigma weight residual 1.527 1.538 -0.011 1.31e-02 5.83e+03 7.69e-01 bond pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta sigma weight residual 1.469 1.475 -0.006 7.40e-03 1.83e+04 7.17e-01 bond pdb=" C LEU A 788 " pdb=" N PRO A 789 " ideal model delta sigma weight residual 1.336 1.326 0.010 1.20e-02 6.94e+03 6.91e-01 ... (remaining 15075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 24433 1.04 - 2.09: 1340 2.09 - 3.13: 85 3.13 - 4.17: 38 4.17 - 5.22: 2 Bond angle restraints: 25898 Sorted by residual: angle pdb=" N ILE A 307 " pdb=" CA ILE A 307 " pdb=" C ILE A 307 " ideal model delta sigma weight residual 113.20 109.25 3.95 9.60e-01 1.09e+00 1.69e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 111.88 107.56 4.32 1.06e+00 8.90e-01 1.66e+01 angle pdb=" N ASN A 675 " pdb=" CA ASN A 675 " pdb=" CB ASN A 675 " ideal model delta sigma weight residual 114.17 110.43 3.74 1.14e+00 7.69e-01 1.08e+01 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 111.81 109.56 2.25 8.60e-01 1.35e+00 6.83e+00 angle pdb=" N GLY B 41 " pdb=" CA GLY B 41 " pdb=" C GLY B 41 " ideal model delta sigma weight residual 111.21 113.84 -2.63 1.04e+00 9.25e-01 6.38e+00 ... (remaining 25893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 6862 15.53 - 31.07: 457 31.07 - 46.60: 118 46.60 - 62.14: 55 62.14 - 77.67: 4 Dihedral angle restraints: 7496 sinusoidal: 3842 harmonic: 3654 Sorted by residual: dihedral pdb=" CA VAL A 756 " pdb=" C VAL A 756 " pdb=" N ASP A 757 " pdb=" CA ASP A 757 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PHE A 783 " pdb=" C PHE A 783 " pdb=" N PRO A 784 " pdb=" CA PRO A 784 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASN A 675 " pdb=" C ASN A 675 " pdb=" N PHE A 676 " pdb=" CA PHE A 676 " ideal model delta harmonic sigma weight residual 180.00 163.56 16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 7493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 889 0.029 - 0.058: 326 0.058 - 0.087: 81 0.087 - 0.115: 71 0.115 - 0.144: 13 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE A 796 " pdb=" N ILE A 796 " pdb=" C ILE A 796 " pdb=" CB ILE A 796 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA VAL A 749 " pdb=" N VAL A 749 " pdb=" C VAL A 749 " pdb=" CB VAL A 749 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1377 not shown) Planarity restraints: 2299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 783 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 784 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 784 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 784 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 835 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 836 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 836 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 836 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 370 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 371 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.018 5.00e-02 4.00e+02 ... (remaining 2296 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 3292 2.31 - 2.89: 29215 2.89 - 3.46: 33909 3.46 - 4.03: 46085 4.03 - 4.60: 68707 Nonbonded interactions: 181208 Sorted by model distance: nonbonded pdb=" O GLN A 662 " pdb="HD22 ASN A 666 " model vdw 1.742 2.450 nonbonded pdb=" HA GLN A 662 " pdb="HE22 GLN A 662 " model vdw 1.799 2.270 nonbonded pdb="HH22 ARG A 359 " pdb=" H SER A 404 " model vdw 1.823 2.100 nonbonded pdb=" HG1 THR A 716 " pdb=" H VAL A 718 " model vdw 1.838 2.100 nonbonded pdb="HD21 ASN A 333 " pdb=" HE1 TYR A 335 " model vdw 1.877 2.100 ... (remaining 181203 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.970 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: 0.090 Extract box with map and model: 0.320 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 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 : 0.003 0.026 9146 Z= 0.147 Angle : 0.519 5.218 12381 Z= 0.296 Chirality : 0.039 0.144 1380 Planarity : 0.003 0.040 1612 Dihedral : 11.118 76.159 3431 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 40.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.02 % Favored : 91.80 % Rotamer: Outliers : 3.35 % Allowed : 8.22 % Favored : 88.44 % 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 are not related in a simple way. whole: -1.71 (0.25), residues: 1122 helix: 0.60 (0.30), residues: 295 sheet: -2.18 (0.35), residues: 205 loop : -1.64 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.010 0.001 TYR A 157 PHE 0.012 0.001 PHE A 401 TRP 0.005 0.001 TRP B 297 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9146) covalent geometry : angle 0.51894 (12381) hydrogen bonds : bond 0.17648 ( 291) hydrogen bonds : angle 7.21836 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.6417 (ttp) cc_final: 0.6143 (ttm) REVERT: A 176 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7551 (tm) REVERT: B 45 MET cc_start: 0.1824 (mtm) cc_final: 0.1185 (mmp) REVERT: B 135 VAL cc_start: -0.0325 (OUTLIER) cc_final: -0.0608 (p) REVERT: B 318 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5489 (mm) outliers start: 33 outliers final: 11 residues processed: 192 average time/residue: 0.2272 time to fit residues: 55.9628 Evaluate side-chains 116 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** 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 = 0.3870 r_free = 0.3870 target = 0.096231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066614 restraints weight = 95305.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069760 restraints weight = 46846.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071841 restraints weight = 29150.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.073172 restraints weight = 21022.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073743 restraints weight = 16753.143| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9146 Z= 0.156 Angle : 0.551 5.176 12381 Z= 0.295 Chirality : 0.041 0.176 1380 Planarity : 0.005 0.058 1612 Dihedral : 4.410 24.769 1236 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 40.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.91 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 are not related in a simple way. whole: -1.64 (0.25), residues: 1122 helix: 0.71 (0.31), residues: 300 sheet: -1.97 (0.36), residues: 204 loop : -1.73 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 874 TYR 0.017 0.001 TYR A 596 PHE 0.035 0.002 PHE A 704 TRP 0.008 0.001 TRP B 297 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9146) covalent geometry : angle 0.55054 (12381) hydrogen bonds : bond 0.03888 ( 291) hydrogen bonds : angle 5.77335 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9375 (mt) cc_final: 0.9052 (mp) REVERT: A 296 PHE cc_start: 0.8868 (t80) cc_final: 0.8651 (t80) REVERT: A 300 LEU cc_start: 0.9329 (mt) cc_final: 0.9113 (mt) REVERT: A 319 MET cc_start: 0.8776 (mmm) cc_final: 0.8561 (mmm) REVERT: A 327 PHE cc_start: 0.8767 (m-80) cc_final: 0.8404 (m-80) REVERT: A 787 VAL cc_start: 0.9222 (t) cc_final: 0.8877 (t) REVERT: A 788 LEU cc_start: 0.9284 (tp) cc_final: 0.9058 (tp) REVERT: B 45 MET cc_start: 0.2940 (mtm) cc_final: 0.2003 (mmp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2227 time to fit residues: 35.3618 Evaluate side-chains 88 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 0.0270 chunk 46 optimal weight: 6.9990 chunk 81 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.094629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065197 restraints weight = 95849.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068077 restraints weight = 49155.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.069936 restraints weight = 31687.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071210 restraints weight = 23445.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071895 restraints weight = 19024.367| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9146 Z= 0.210 Angle : 0.573 5.054 12381 Z= 0.306 Chirality : 0.040 0.155 1380 Planarity : 0.004 0.050 1612 Dihedral : 4.659 22.657 1236 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 44.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.78 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 are not related in a simple way. whole: -1.86 (0.25), residues: 1122 helix: 0.40 (0.30), residues: 302 sheet: -1.89 (0.37), residues: 187 loop : -1.90 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 390 TYR 0.011 0.002 TYR A 659 PHE 0.027 0.002 PHE A 327 TRP 0.008 0.001 TRP B 297 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9146) covalent geometry : angle 0.57271 (12381) hydrogen bonds : bond 0.03993 ( 291) hydrogen bonds : angle 5.77555 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9466 (mt) cc_final: 0.9170 (mp) REVERT: A 146 ASN cc_start: 0.8759 (t0) cc_final: 0.8515 (t0) REVERT: A 178 MET cc_start: 0.9332 (ttm) cc_final: 0.9067 (ttm) REVERT: A 409 ILE cc_start: 0.9417 (mt) cc_final: 0.9162 (tt) REVERT: A 462 ARG cc_start: 0.8907 (mmm-85) cc_final: 0.8706 (mtp85) REVERT: A 672 VAL cc_start: 0.9357 (t) cc_final: 0.9081 (t) REVERT: A 788 LEU cc_start: 0.9442 (tp) cc_final: 0.9185 (tp) REVERT: B 45 MET cc_start: 0.3007 (mtm) cc_final: 0.2076 (mmp) REVERT: B 262 MET cc_start: 0.6210 (ttm) cc_final: 0.5810 (ttm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2117 time to fit residues: 31.4881 Evaluate side-chains 78 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.094362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.064695 restraints weight = 97575.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067787 restraints weight = 48834.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069761 restraints weight = 30823.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071064 restraints weight = 22742.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.071797 restraints weight = 18355.885| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9146 Z= 0.166 Angle : 0.528 5.142 12381 Z= 0.280 Chirality : 0.040 0.145 1380 Planarity : 0.004 0.049 1612 Dihedral : 4.510 22.693 1236 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 43.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.27 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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 are not related in a simple way. whole: -1.79 (0.25), residues: 1122 helix: 0.49 (0.30), residues: 303 sheet: -1.84 (0.37), residues: 187 loop : -1.88 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 390 TYR 0.009 0.001 TYR A 692 PHE 0.014 0.001 PHE A 327 TRP 0.006 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9146) covalent geometry : angle 0.52827 (12381) hydrogen bonds : bond 0.03491 ( 291) hydrogen bonds : angle 5.52555 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9475 (mt) cc_final: 0.9176 (mp) REVERT: A 672 VAL cc_start: 0.9317 (t) cc_final: 0.9026 (t) REVERT: A 788 LEU cc_start: 0.9482 (tp) cc_final: 0.9199 (tp) REVERT: B 45 MET cc_start: 0.3071 (mtm) cc_final: 0.2142 (mmp) REVERT: B 262 MET cc_start: 0.6176 (ttm) cc_final: 0.5853 (ttm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1801 time to fit residues: 25.6463 Evaluate side-chains 78 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 102 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 259 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 = 0.3858 r_free = 0.3858 target = 0.095254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.066355 restraints weight = 98216.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069483 restraints weight = 48789.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.071515 restraints weight = 30449.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.072617 restraints weight = 22138.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073558 restraints weight = 18145.942| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9146 Z= 0.124 Angle : 0.493 5.318 12381 Z= 0.258 Chirality : 0.039 0.150 1380 Planarity : 0.004 0.047 1612 Dihedral : 4.280 20.807 1236 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 40.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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 are not related in a simple way. whole: -1.53 (0.25), residues: 1122 helix: 0.86 (0.30), residues: 297 sheet: -1.80 (0.36), residues: 208 loop : -1.71 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 149 TYR 0.008 0.001 TYR A 746 PHE 0.016 0.001 PHE A 327 TRP 0.004 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9146) covalent geometry : angle 0.49344 (12381) hydrogen bonds : bond 0.03162 ( 291) hydrogen bonds : angle 5.28149 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9450 (mt) cc_final: 0.9172 (mp) REVERT: A 672 VAL cc_start: 0.9309 (t) cc_final: 0.9030 (t) REVERT: A 788 LEU cc_start: 0.9498 (tp) cc_final: 0.9212 (tp) REVERT: B 45 MET cc_start: 0.2933 (mtm) cc_final: 0.2062 (mmp) REVERT: B 262 MET cc_start: 0.6237 (ttm) cc_final: 0.5841 (ttm) REVERT: G 38 MET cc_start: 0.1751 (mtt) cc_final: 0.1310 (mtt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2241 time to fit residues: 30.8620 Evaluate side-chains 81 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 16 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.093968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065097 restraints weight = 96702.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068019 restraints weight = 48738.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069915 restraints weight = 31116.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070921 restraints weight = 22965.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071844 restraints weight = 18954.718| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9146 Z= 0.159 Angle : 0.521 5.167 12381 Z= 0.273 Chirality : 0.039 0.164 1380 Planarity : 0.004 0.047 1612 Dihedral : 4.319 23.448 1236 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 41.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.36 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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 are not related in a simple way. whole: -1.63 (0.25), residues: 1122 helix: 0.69 (0.30), residues: 297 sheet: -1.79 (0.36), residues: 208 loop : -1.75 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 298 TYR 0.010 0.001 TYR A 692 PHE 0.016 0.001 PHE A 690 TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9146) covalent geometry : angle 0.52074 (12381) hydrogen bonds : bond 0.03332 ( 291) hydrogen bonds : angle 5.31537 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9498 (mt) cc_final: 0.9228 (mp) REVERT: A 739 SER cc_start: 0.9168 (p) cc_final: 0.8945 (t) REVERT: A 788 LEU cc_start: 0.9544 (tp) cc_final: 0.9253 (tp) REVERT: B 45 MET cc_start: 0.3267 (mtm) cc_final: 0.2214 (mmp) REVERT: B 262 MET cc_start: 0.6312 (ttm) cc_final: 0.5984 (ttm) REVERT: G 38 MET cc_start: 0.1791 (mtt) cc_final: 0.1404 (mtt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2022 time to fit residues: 27.0253 Evaluate side-chains 79 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.091382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062444 restraints weight = 97826.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065110 restraints weight = 50526.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066857 restraints weight = 33117.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.068044 restraints weight = 24780.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068746 restraints weight = 20327.413| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9146 Z= 0.267 Angle : 0.631 6.848 12381 Z= 0.339 Chirality : 0.041 0.152 1380 Planarity : 0.005 0.058 1612 Dihedral : 4.937 30.275 1236 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 49.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.01 % Favored : 86.90 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.24), residues: 1122 helix: 0.00 (0.29), residues: 302 sheet: -1.79 (0.36), residues: 210 loop : -2.15 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 44 TYR 0.017 0.002 TYR A 692 PHE 0.020 0.002 PHE A 676 TRP 0.013 0.002 TRP B 211 HIS 0.006 0.002 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 9146) covalent geometry : angle 0.63079 (12381) hydrogen bonds : bond 0.04012 ( 291) hydrogen bonds : angle 5.93696 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9533 (mt) cc_final: 0.9280 (mp) REVERT: A 349 MET cc_start: 0.7836 (tpp) cc_final: 0.7574 (tpp) REVERT: A 360 CYS cc_start: 0.9022 (t) cc_final: 0.8771 (t) REVERT: A 617 MET cc_start: 0.8459 (ttm) cc_final: 0.8179 (ttp) REVERT: B 45 MET cc_start: 0.3333 (mtm) cc_final: 0.2271 (mmp) REVERT: G 38 MET cc_start: 0.2171 (mtt) cc_final: 0.1749 (mtt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1867 time to fit residues: 25.6077 Evaluate side-chains 77 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.093835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.064811 restraints weight = 96495.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.067837 restraints weight = 47927.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069794 restraints weight = 30031.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.071142 restraints weight = 21757.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071829 restraints weight = 17293.777| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9146 Z= 0.104 Angle : 0.510 5.627 12381 Z= 0.266 Chirality : 0.039 0.156 1380 Planarity : 0.004 0.053 1612 Dihedral : 4.448 24.387 1236 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 41.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.93 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 are not related in a simple way. whole: -1.62 (0.25), residues: 1122 helix: 0.76 (0.30), residues: 296 sheet: -1.65 (0.37), residues: 202 loop : -1.84 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.008 0.001 TYR A 596 PHE 0.028 0.001 PHE A 327 TRP 0.006 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9146) covalent geometry : angle 0.51027 (12381) hydrogen bonds : bond 0.03090 ( 291) hydrogen bonds : angle 5.26434 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9486 (mt) cc_final: 0.9243 (mp) REVERT: A 617 MET cc_start: 0.8233 (ttm) cc_final: 0.7937 (ttp) REVERT: A 672 VAL cc_start: 0.9182 (t) cc_final: 0.8888 (t) REVERT: B 45 MET cc_start: 0.3002 (mtm) cc_final: 0.2098 (mmp) REVERT: B 262 MET cc_start: 0.6713 (ttm) cc_final: 0.6312 (ttm) REVERT: G 38 MET cc_start: 0.2181 (mtt) cc_final: 0.1769 (mtt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1967 time to fit residues: 27.8153 Evaluate side-chains 79 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 78 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 259 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 = 0.3847 r_free = 0.3847 target = 0.094390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.065368 restraints weight = 95569.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068446 restraints weight = 46916.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.070489 restraints weight = 29204.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071848 restraints weight = 21047.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072359 restraints weight = 16585.838| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9146 Z= 0.096 Angle : 0.497 6.331 12381 Z= 0.255 Chirality : 0.039 0.156 1380 Planarity : 0.004 0.051 1612 Dihedral : 4.197 21.931 1236 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 39.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.11 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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 are not related in a simple way. whole: -1.36 (0.26), residues: 1122 helix: 1.07 (0.31), residues: 297 sheet: -1.62 (0.37), residues: 197 loop : -1.68 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 149 TYR 0.007 0.001 TYR A 596 PHE 0.021 0.001 PHE A 327 TRP 0.016 0.001 TRP A 665 HIS 0.003 0.001 HIS A 821 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9146) covalent geometry : angle 0.49698 (12381) hydrogen bonds : bond 0.02871 ( 291) hydrogen bonds : angle 5.03891 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9491 (mt) cc_final: 0.9272 (mp) REVERT: A 462 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8767 (mmm-85) REVERT: A 672 VAL cc_start: 0.9122 (t) cc_final: 0.8830 (t) REVERT: B 45 MET cc_start: 0.2924 (mtm) cc_final: 0.2058 (mmp) REVERT: B 262 MET cc_start: 0.6545 (ttm) cc_final: 0.6199 (ttm) REVERT: G 28 ILE cc_start: 0.8664 (tp) cc_final: 0.8108 (pt) REVERT: G 38 MET cc_start: 0.2148 (mtt) cc_final: 0.1603 (mtt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2059 time to fit residues: 28.3332 Evaluate side-chains 82 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 96 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.094114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065213 restraints weight = 95360.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068260 restraints weight = 46802.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.070298 restraints weight = 29246.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.071400 restraints weight = 21008.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.072409 restraints weight = 16990.663| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9146 Z= 0.103 Angle : 0.494 6.760 12381 Z= 0.253 Chirality : 0.039 0.146 1380 Planarity : 0.003 0.050 1612 Dihedral : 4.112 21.914 1236 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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 are not related in a simple way. whole: -1.27 (0.26), residues: 1122 helix: 1.15 (0.31), residues: 297 sheet: -1.57 (0.37), residues: 197 loop : -1.64 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.008 0.001 TYR A 596 PHE 0.019 0.001 PHE A 327 TRP 0.013 0.001 TRP A 665 HIS 0.002 0.001 HIS A 821 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9146) covalent geometry : angle 0.49409 (12381) hydrogen bonds : bond 0.02813 ( 291) hydrogen bonds : angle 4.93283 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9491 (mt) cc_final: 0.9273 (mp) REVERT: A 462 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8742 (mmm-85) REVERT: A 672 VAL cc_start: 0.9088 (t) cc_final: 0.8802 (t) REVERT: B 45 MET cc_start: 0.2990 (mtm) cc_final: 0.2081 (mmp) REVERT: B 262 MET cc_start: 0.6580 (ttm) cc_final: 0.6196 (ttm) REVERT: G 38 MET cc_start: 0.2162 (mtt) cc_final: 0.1637 (mtt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2009 time to fit residues: 27.0519 Evaluate side-chains 79 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 43 optimal weight: 0.0670 chunk 65 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 81 optimal weight: 9.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.094787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.066047 restraints weight = 95010.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069126 restraints weight = 46203.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071120 restraints weight = 28725.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.072464 restraints weight = 20617.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.073032 restraints weight = 16365.841| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9146 Z= 0.084 Angle : 0.490 7.865 12381 Z= 0.247 Chirality : 0.039 0.149 1380 Planarity : 0.003 0.050 1612 Dihedral : 3.962 20.351 1236 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 37.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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 are not related in a simple way. whole: -1.11 (0.26), residues: 1122 helix: 1.28 (0.31), residues: 297 sheet: -1.49 (0.38), residues: 197 loop : -1.52 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 149 TYR 0.007 0.001 TYR A 596 PHE 0.019 0.001 PHE A 327 TRP 0.012 0.001 TRP A 665 HIS 0.003 0.001 HIS A 821 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 9146) covalent geometry : angle 0.49010 (12381) hydrogen bonds : bond 0.02640 ( 291) hydrogen bonds : angle 4.75219 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3281.86 seconds wall clock time: 56 minutes 55.80 seconds (3415.80 seconds total)