Starting phenix.real_space_refine on Fri Aug 22 19:56:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f3f_50173/08_2025/9f3f_50173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f3f_50173/08_2025/9f3f_50173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f3f_50173/08_2025/9f3f_50173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f3f_50173/08_2025/9f3f_50173.map" model { file = "/net/cci-nas-00/data/ceres_data/9f3f_50173/08_2025/9f3f_50173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f3f_50173/08_2025/9f3f_50173.cif" } resolution = 2.4 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 43 5.16 5 C 4781 2.51 5 N 1307 2.21 5 O 1364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7496 Number of models: 1 Model: "" Number of chains: 4 Chain: "1" Number of atoms: 5933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5933 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 15 Chain: "2" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1134 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 1 Chain: "3" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 404 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "2" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.02, per 1000 atoms: 0.27 Number of scatterers: 7496 At special positions: 0 Unit cell: (81.27, 86.1462, 107.276, 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 43 16.00 P 1 15.00 O 1364 8.00 N 1307 7.00 C 4781 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: 0.71 Conformation dependent library (CDL) restraints added in 399.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 63.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain '1' and resid 44 through 54 Processing helix chain '1' and resid 55 through 62 Proline residue: 1 60 - end of helix Processing helix chain '1' and resid 91 through 98 removed outlier: 3.575A pdb=" N LEU 1 98 " --> pdb=" O GLU 1 94 " (cutoff:3.500A) Processing helix chain '1' and resid 109 through 114 removed outlier: 3.518A pdb=" N GLY 1 113 " --> pdb=" O SER 1 109 " (cutoff:3.500A) Processing helix chain '1' and resid 120 through 125 Processing helix chain '1' and resid 149 through 165 Processing helix chain '1' and resid 178 through 191 Processing helix chain '1' and resid 213 through 223 removed outlier: 3.816A pdb=" N PHE 1 219 " --> pdb=" O LEU 1 215 " (cutoff:3.500A) Processing helix chain '1' and resid 254 through 276 removed outlier: 3.644A pdb=" N LEU 1 266 " --> pdb=" O ASN 1 262 " (cutoff:3.500A) Processing helix chain '1' and resid 278 through 291 Processing helix chain '1' and resid 295 through 321 removed outlier: 3.511A pdb=" N VAL 1 299 " --> pdb=" O ALA 1 295 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP 1 300 " --> pdb=" O PRO 1 296 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA 1 301 " --> pdb=" O GLU 1 297 " (cutoff:3.500A) Processing helix chain '1' and resid 328 through 349 Processing helix chain '1' and resid 363 through 385 Processing helix chain '1' and resid 389 through 394 Processing helix chain '1' and resid 411 through 420 Processing helix chain '1' and resid 420 through 429 Processing helix chain '1' and resid 434 through 447 removed outlier: 3.765A pdb=" N ARG 1 447 " --> pdb=" O LYS 1 443 " (cutoff:3.500A) Processing helix chain '1' and resid 462 through 476 removed outlier: 3.600A pdb=" N ARG 1 476 " --> pdb=" O VAL 1 472 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 487 removed outlier: 3.560A pdb=" N LEU 1 483 " --> pdb=" O TYR 1 479 " (cutoff:3.500A) Processing helix chain '1' and resid 488 through 490 No H-bonds generated for 'chain '1' and resid 488 through 490' Processing helix chain '1' and resid 491 through 499 Processing helix chain '1' and resid 533 through 552 removed outlier: 4.116A pdb=" N VAL 1 539 " --> pdb=" O THR 1 535 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU 1 540 " --> pdb=" O ALA 1 536 " (cutoff:3.500A) Proline residue: 1 549 - end of helix Processing helix chain '1' and resid 553 through 566 Processing helix chain '1' and resid 568 through 577 Processing helix chain '1' and resid 602 through 627 Processing helix chain '1' and resid 630 through 653 Proline residue: 1 643 - end of helix Proline residue: 1 651 - end of helix Processing helix chain '1' and resid 683 through 692 Processing helix chain '1' and resid 698 through 701 Processing helix chain '1' and resid 702 through 714 removed outlier: 3.605A pdb=" N GLU 1 714 " --> pdb=" O HIS 1 710 " (cutoff:3.500A) Processing helix chain '1' and resid 739 through 748 Processing helix chain '1' and resid 766 through 779 removed outlier: 3.548A pdb=" N LEU 1 779 " --> pdb=" O ARG 1 775 " (cutoff:3.500A) Processing helix chain '1' and resid 837 through 849 Processing helix chain '1' and resid 851 through 856 Processing helix chain '1' and resid 866 through 892 Processing helix chain '1' and resid 900 through 904 Processing helix chain '1' and resid 913 through 937 removed outlier: 3.811A pdb=" N ARG 1 917 " --> pdb=" O VAL 1 913 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG 1 924 " --> pdb=" O ILE 1 920 " (cutoff:3.500A) Processing helix chain '1' and resid 941 through 965 Processing helix chain '1' and resid 979 through 985 Processing helix chain '1' and resid 987 through 997 Processing helix chain '2' and resid 5 through 9 removed outlier: 3.546A pdb=" N LEU 2 8 " --> pdb=" O LEU 2 5 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 22 Processing helix chain '2' and resid 29 through 39 removed outlier: 3.765A pdb=" N GLU 2 36 " --> pdb=" O GLU 2 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN 2 37 " --> pdb=" O ARG 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 63 Processing helix chain '2' and resid 92 through 103 removed outlier: 3.603A pdb=" N ALA 2 96 " --> pdb=" O SER 2 92 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 58 removed outlier: 3.604A pdb=" N TRP 3 48 " --> pdb=" O ILE 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 64 through 70 Processing sheet with id=AA1, first strand: chain '1' and resid 245 through 246 removed outlier: 4.757A pdb=" N THR 1 404 " --> pdb=" O ALA 1 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 409 through 410 removed outlier: 4.798A pdb=" N LEU 1 409 " --> pdb=" O VAL 1 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 663 through 664 removed outlier: 3.506A pdb=" N ASP 1 681 " --> pdb=" O ILE 1 664 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 787 through 788 removed outlier: 4.610A pdb=" N ASP 1 787 " --> pdb=" O HIS 1 833 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 43 through 45 removed outlier: 6.967A pdb=" N CYS 2 83 " --> pdb=" O SER 2 76 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER 2 76 " --> pdb=" O CYS 2 83 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE 2 85 " --> pdb=" O GLY 2 74 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLY 2 128 " --> pdb=" O MET 2 73 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU 2 75 " --> pdb=" O GLY 2 128 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1170 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: 1.23 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1365 1.32 - 1.45: 1951 1.45 - 1.57: 4279 1.57 - 1.69: 1 1.69 - 1.82: 64 Bond restraints: 7660 Sorted by residual: bond pdb=" CA SER 1 109 " pdb=" CB SER 1 109 " ideal model delta sigma weight residual 1.533 1.464 0.069 1.51e-02 4.39e+03 2.08e+01 bond pdb=" N ILE 2 176 " pdb=" CA ILE 2 176 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.08e+01 bond pdb=" CA SER 1 280 " pdb=" CB SER 1 280 " ideal model delta sigma weight residual 1.528 1.460 0.068 1.56e-02 4.11e+03 1.93e+01 bond pdb=" CA GLY 2 74 " pdb=" C GLY 2 74 " ideal model delta sigma weight residual 1.516 1.481 0.035 8.90e-03 1.26e+04 1.55e+01 bond pdb=" N ARG 1 59 " pdb=" CA ARG 1 59 " ideal model delta sigma weight residual 1.462 1.492 -0.029 7.70e-03 1.69e+04 1.46e+01 ... (remaining 7655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 9609 2.24 - 4.48: 684 4.48 - 6.72: 92 6.72 - 8.96: 11 8.96 - 11.20: 3 Bond angle restraints: 10399 Sorted by residual: angle pdb=" N ALA 2 2 " pdb=" CA ALA 2 2 " pdb=" C ALA 2 2 " ideal model delta sigma weight residual 113.28 102.08 11.20 1.57e+00 4.06e-01 5.09e+01 angle pdb=" N GLU 2 3 " pdb=" CA GLU 2 3 " pdb=" C GLU 2 3 " ideal model delta sigma weight residual 113.17 104.79 8.38 1.26e+00 6.30e-01 4.42e+01 angle pdb=" N ASN 2 39 " pdb=" CA ASN 2 39 " pdb=" C ASN 2 39 " ideal model delta sigma weight residual 113.01 106.08 6.93 1.20e+00 6.94e-01 3.34e+01 angle pdb=" N THR 2 42 " pdb=" CA THR 2 42 " pdb=" C THR 2 42 " ideal model delta sigma weight residual 112.41 105.32 7.09 1.30e+00 5.92e-01 2.98e+01 angle pdb=" CA PHE 2 85 " pdb=" CB PHE 2 85 " pdb=" CG PHE 2 85 " ideal model delta sigma weight residual 113.80 119.24 -5.44 1.00e+00 1.00e+00 2.96e+01 ... (remaining 10394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4028 17.86 - 35.73: 390 35.73 - 53.59: 103 53.59 - 71.46: 31 71.46 - 89.32: 10 Dihedral angle restraints: 4562 sinusoidal: 1830 harmonic: 2732 Sorted by residual: dihedral pdb=" CA LEU 1 531 " pdb=" C LEU 1 531 " pdb=" N TYR 1 532 " pdb=" CA TYR 1 532 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" C VAL 2 46 " pdb=" N VAL 2 46 " pdb=" CA VAL 2 46 " pdb=" CB VAL 2 46 " ideal model delta harmonic sigma weight residual -122.00 -132.20 10.20 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" CA PRO 1 144 " pdb=" C PRO 1 144 " pdb=" N ARG 1 145 " pdb=" CA ARG 1 145 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 907 0.064 - 0.128: 201 0.128 - 0.192: 59 0.192 - 0.256: 14 0.256 - 0.320: 6 Chirality restraints: 1187 Sorted by residual: chirality pdb=" CB VAL 1 146 " pdb=" CA VAL 1 146 " pdb=" CG1 VAL 1 146 " pdb=" CG2 VAL 1 146 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA GLU 2 3 " pdb=" N GLU 2 3 " pdb=" C GLU 2 3 " pdb=" CB GLU 2 3 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA VAL 1 571 " pdb=" N VAL 1 571 " pdb=" C VAL 1 571 " pdb=" CB VAL 1 571 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1184 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER 1 166 " -0.026 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C SER 1 166 " 0.094 2.00e-02 2.50e+03 pdb=" O SER 1 166 " -0.036 2.00e-02 2.50e+03 pdb=" N TRP 1 167 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 125 " 0.276 9.50e-02 1.11e+02 1.24e-01 9.41e+00 pdb=" NE ARG 2 125 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG 2 125 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 125 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 125 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 1 180 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C ASP 1 180 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP 1 180 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL 1 181 " 0.016 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 449 2.72 - 3.27: 7773 3.27 - 3.81: 13036 3.81 - 4.36: 16540 4.36 - 4.90: 27125 Nonbonded interactions: 64923 Sorted by model distance: nonbonded pdb=" O SER 1 101 " pdb=" OG SER 1 101 " model vdw 2.180 3.040 nonbonded pdb=" OD1 ASP 1 681 " pdb=" N LEU 1 682 " model vdw 2.184 3.120 nonbonded pdb=" O ASN 1 497 " pdb=" OG SER 1 767 " model vdw 2.204 3.040 nonbonded pdb=" O VAL 1 934 " pdb=" OG SER 1 937 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR 2 79 " pdb=" OG1 THR 2 81 " model vdw 2.228 3.040 ... (remaining 64918 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: 2.910 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.750 Find NCS groups from input model: 0.030 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:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.008 0.069 7660 Z= 0.516 Angle : 1.184 11.204 10399 Z= 0.808 Chirality : 0.066 0.320 1187 Planarity : 0.010 0.124 1312 Dihedral : 16.339 89.320 2780 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.45 % Allowed : 21.23 % Favored : 76.32 % Cbeta Deviations : 0.11 % 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: -0.13 (0.27), residues: 901 helix: 0.62 (0.22), residues: 536 sheet: -4.93 (0.74), residues: 10 loop : -0.94 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 526 TYR 0.028 0.003 TYR 2 4 PHE 0.023 0.002 PHE 1 51 TRP 0.047 0.003 TRP 1 111 HIS 0.009 0.001 HIS 1 163 Details of bonding type rmsd covalent geometry : bond 0.00772 ( 7660) covalent geometry : angle 1.18404 (10399) hydrogen bonds : bond 0.14873 ( 396) hydrogen bonds : angle 6.49143 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 216 GLU cc_start: 0.7728 (tp30) cc_final: 0.7452 (tp30) REVERT: 2 127 TRP cc_start: 0.8624 (m100) cc_final: 0.8350 (m100) outliers start: 20 outliers final: 3 residues processed: 180 average time/residue: 0.6126 time to fit residues: 115.7247 Evaluate side-chains 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 539 VAL Chi-restraints excluded: chain 1 residue 683 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 412 HIS 1 640 GLN 2 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.090967 restraints weight = 12460.468| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.46 r_work: 0.3299 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7660 Z= 0.152 Angle : 0.613 7.687 10399 Z= 0.314 Chirality : 0.039 0.216 1187 Planarity : 0.005 0.057 1312 Dihedral : 4.265 23.695 1031 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.29 % Allowed : 22.33 % Favored : 73.37 % 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: 0.81 (0.28), residues: 901 helix: 1.38 (0.22), residues: 561 sheet: -3.77 (0.97), residues: 10 loop : -0.75 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 440 TYR 0.022 0.002 TYR 2 4 PHE 0.009 0.001 PHE 1 776 TRP 0.016 0.001 TRP 1 57 HIS 0.006 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7660) covalent geometry : angle 0.61264 (10399) hydrogen bonds : bond 0.04361 ( 396) hydrogen bonds : angle 5.00589 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: 1 216 GLU cc_start: 0.8108 (tp30) cc_final: 0.7720 (tp30) REVERT: 1 393 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: 1 605 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7999 (mt-10) REVERT: 1 688 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7999 (tpp) REVERT: 1 766 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8143 (p) REVERT: 1 948 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7873 (mm110) REVERT: 2 80 ARG cc_start: 0.8627 (mtm180) cc_final: 0.8391 (ttm170) REVERT: 3 71 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6317 (mt-10) outliers start: 35 outliers final: 6 residues processed: 133 average time/residue: 0.5284 time to fit residues: 74.2188 Evaluate side-chains 105 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 287 LEU Chi-restraints excluded: chain 1 residue 393 GLU Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 1 residue 683 THR Chi-restraints excluded: chain 1 residue 688 MET Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 191 GLN ** 1 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 640 GLN ** 2 39 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 = 0.3806 r_free = 0.3806 target = 0.112838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091005 restraints weight = 12314.595| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.43 r_work: 0.3289 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7660 Z= 0.129 Angle : 0.564 6.860 10399 Z= 0.285 Chirality : 0.039 0.144 1187 Planarity : 0.005 0.051 1312 Dihedral : 4.036 22.461 1029 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.29 % Allowed : 21.72 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.28), residues: 901 helix: 1.72 (0.22), residues: 553 sheet: -3.17 (0.96), residues: 17 loop : -0.53 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 563 TYR 0.015 0.001 TYR 2 4 PHE 0.010 0.001 PHE 1 51 TRP 0.011 0.001 TRP 1 111 HIS 0.007 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7660) covalent geometry : angle 0.56395 (10399) hydrogen bonds : bond 0.03908 ( 396) hydrogen bonds : angle 4.69395 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7864 (t0) REVERT: 1 216 GLU cc_start: 0.8086 (tp30) cc_final: 0.7823 (tp30) REVERT: 1 393 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: 1 605 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7954 (mt-10) REVERT: 1 766 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8109 (p) REVERT: 1 948 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7854 (mm110) REVERT: 2 5 LEU cc_start: 0.8085 (tt) cc_final: 0.7697 (tt) REVERT: 2 64 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6786 (mmm160) REVERT: 2 80 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8285 (ttm170) outliers start: 35 outliers final: 10 residues processed: 131 average time/residue: 0.5233 time to fit residues: 72.6509 Evaluate side-chains 104 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 241 LEU Chi-restraints excluded: chain 1 residue 278 VAL Chi-restraints excluded: chain 1 residue 287 LEU Chi-restraints excluded: chain 1 residue 393 GLU Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 845 MET Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 977 VAL Chi-restraints excluded: chain 2 residue 64 ARG Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 640 GLN 2 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.109449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087179 restraints weight = 12737.949| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.49 r_work: 0.3236 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7660 Z= 0.189 Angle : 0.590 6.311 10399 Z= 0.302 Chirality : 0.041 0.227 1187 Planarity : 0.005 0.053 1312 Dihedral : 4.135 23.965 1028 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.79 % Allowed : 21.35 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.28), residues: 901 helix: 1.71 (0.22), residues: 548 sheet: -3.17 (0.92), residues: 17 loop : -0.55 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 604 TYR 0.014 0.002 TYR 2 4 PHE 0.038 0.002 PHE 2 30 TRP 0.010 0.001 TRP 1 57 HIS 0.006 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7660) covalent geometry : angle 0.59010 (10399) hydrogen bonds : bond 0.04278 ( 396) hydrogen bonds : angle 4.74061 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7783 (t0) REVERT: 1 216 GLU cc_start: 0.8220 (tp30) cc_final: 0.7788 (tp30) REVERT: 1 389 ARG cc_start: 0.8167 (mpt180) cc_final: 0.7804 (mpp-170) REVERT: 1 664 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8742 (pp) REVERT: 1 766 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8206 (p) REVERT: 1 948 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7876 (mm110) REVERT: 2 5 LEU cc_start: 0.7838 (tt) cc_final: 0.7379 (tt) REVERT: 2 33 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8082 (ttp80) REVERT: 2 64 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.6809 (mmm160) REVERT: 2 80 ARG cc_start: 0.8658 (mtm180) cc_final: 0.8444 (ttm170) REVERT: 3 71 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6584 (mt-10) outliers start: 39 outliers final: 13 residues processed: 129 average time/residue: 0.4739 time to fit residues: 65.0456 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 243 ASP Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 535 THR Chi-restraints excluded: chain 1 residue 567 VAL Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 664 ILE Chi-restraints excluded: chain 1 residue 688 MET Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 902 ILE Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 64 ARG Chi-restraints excluded: chain 2 residue 112 VAL Chi-restraints excluded: chain 3 residue 62 THR Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 191 GLN ** 1 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 640 GLN 1 647 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.106862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084485 restraints weight = 12722.322| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.47 r_work: 0.3186 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 7660 Z= 0.271 Angle : 0.648 8.150 10399 Z= 0.334 Chirality : 0.044 0.181 1187 Planarity : 0.005 0.062 1312 Dihedral : 4.370 30.087 1028 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.42 % Allowed : 21.47 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.89 (0.28), residues: 901 helix: 1.48 (0.22), residues: 547 sheet: -3.43 (0.84), residues: 17 loop : -0.63 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 440 TYR 0.016 0.002 TYR 1 533 PHE 0.016 0.002 PHE 1 275 TRP 0.011 0.002 TRP 1 57 HIS 0.008 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00629 ( 7660) covalent geometry : angle 0.64815 (10399) hydrogen bonds : bond 0.04658 ( 396) hydrogen bonds : angle 4.88246 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7793 (t0) REVERT: 1 216 GLU cc_start: 0.8344 (tp30) cc_final: 0.8043 (tp30) REVERT: 1 533 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8590 (m-80) REVERT: 1 605 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: 1 664 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8730 (pp) REVERT: 1 688 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8008 (tpp) REVERT: 1 766 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8273 (p) REVERT: 1 879 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7920 (mtp180) REVERT: 1 948 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7940 (mm110) REVERT: 2 5 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7371 (tt) REVERT: 2 80 ARG cc_start: 0.8777 (mtm180) cc_final: 0.8512 (ttm170) REVERT: 3 69 GLU cc_start: 0.8659 (tp30) cc_final: 0.8202 (tp30) REVERT: 3 71 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6533 (mt-10) outliers start: 36 outliers final: 12 residues processed: 127 average time/residue: 0.5205 time to fit residues: 70.2140 Evaluate side-chains 118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 243 ASP Chi-restraints excluded: chain 1 residue 420 VAL Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 1 residue 535 THR Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 640 GLN Chi-restraints excluded: chain 1 residue 650 LEU Chi-restraints excluded: chain 1 residue 664 ILE Chi-restraints excluded: chain 1 residue 688 MET Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 879 ARG Chi-restraints excluded: chain 1 residue 902 ILE Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 112 VAL Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.109641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087611 restraints weight = 12683.580| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.47 r_work: 0.3248 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7660 Z= 0.138 Angle : 0.593 10.754 10399 Z= 0.295 Chirality : 0.039 0.136 1187 Planarity : 0.005 0.059 1312 Dihedral : 4.117 26.687 1028 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.19 % Allowed : 23.44 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.28), residues: 901 helix: 1.72 (0.21), residues: 547 sheet: -3.48 (0.83), residues: 17 loop : -0.53 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 604 TYR 0.012 0.001 TYR 1 698 PHE 0.010 0.001 PHE 2 30 TRP 0.011 0.001 TRP 1 57 HIS 0.009 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7660) covalent geometry : angle 0.59273 (10399) hydrogen bonds : bond 0.03910 ( 396) hydrogen bonds : angle 4.63841 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 115 CYS cc_start: 0.8706 (t) cc_final: 0.8411 (m) REVERT: 1 185 ASP cc_start: 0.8869 (m-30) cc_final: 0.8604 (m-30) REVERT: 1 392 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7893 (tpp80) REVERT: 1 393 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: 1 605 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: 1 664 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8702 (pp) REVERT: 1 766 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8134 (p) REVERT: 2 5 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7059 (tt) REVERT: 2 80 ARG cc_start: 0.8709 (mtm180) cc_final: 0.8377 (ttm170) REVERT: 3 69 GLU cc_start: 0.8647 (tp30) cc_final: 0.8144 (tp30) REVERT: 3 71 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6577 (mt-10) outliers start: 26 outliers final: 15 residues processed: 123 average time/residue: 0.4870 time to fit residues: 63.7965 Evaluate side-chains 118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 121 VAL Chi-restraints excluded: chain 1 residue 241 LEU Chi-restraints excluded: chain 1 residue 243 ASP Chi-restraints excluded: chain 1 residue 393 GLU Chi-restraints excluded: chain 1 residue 420 VAL Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 1 residue 535 THR Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 664 ILE Chi-restraints excluded: chain 1 residue 688 MET Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 845 MET Chi-restraints excluded: chain 1 residue 867 SER Chi-restraints excluded: chain 1 residue 902 ILE Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 2 residue 112 VAL Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 14 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 18 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.111423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089366 restraints weight = 12579.201| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.48 r_work: 0.3278 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7660 Z= 0.118 Angle : 0.575 10.664 10399 Z= 0.284 Chirality : 0.038 0.132 1187 Planarity : 0.005 0.055 1312 Dihedral : 3.911 22.741 1028 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.44 % Allowed : 24.42 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.28), residues: 901 helix: 1.86 (0.21), residues: 552 sheet: -3.33 (0.86), residues: 17 loop : -0.48 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 604 TYR 0.012 0.001 TYR 1 698 PHE 0.011 0.001 PHE 1 275 TRP 0.014 0.001 TRP 1 167 HIS 0.009 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7660) covalent geometry : angle 0.57462 (10399) hydrogen bonds : bond 0.03568 ( 396) hydrogen bonds : angle 4.45568 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 185 ASP cc_start: 0.8880 (m-30) cc_final: 0.8613 (m-30) REVERT: 1 605 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: 1 607 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8149 (pp20) REVERT: 1 766 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8073 (p) REVERT: 1 855 SER cc_start: 0.9052 (t) cc_final: 0.8653 (p) REVERT: 1 948 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7911 (mm110) REVERT: 2 5 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6909 (tt) REVERT: 2 64 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.6800 (mmm160) REVERT: 2 80 ARG cc_start: 0.8631 (mtm180) cc_final: 0.8335 (ttm170) REVERT: 3 71 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6619 (mt-10) outliers start: 28 outliers final: 14 residues processed: 122 average time/residue: 0.5290 time to fit residues: 68.2980 Evaluate side-chains 118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 241 LEU Chi-restraints excluded: chain 1 residue 243 ASP Chi-restraints excluded: chain 1 residue 262 ASN Chi-restraints excluded: chain 1 residue 420 VAL Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 1 residue 535 THR Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 607 GLU Chi-restraints excluded: chain 1 residue 664 ILE Chi-restraints excluded: chain 1 residue 688 MET Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 845 MET Chi-restraints excluded: chain 1 residue 867 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 2 residue 64 ARG Chi-restraints excluded: chain 2 residue 112 VAL Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 0.0270 chunk 69 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.110594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088329 restraints weight = 12674.279| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.50 r_work: 0.3261 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7660 Z= 0.138 Angle : 0.598 13.126 10399 Z= 0.291 Chirality : 0.039 0.244 1187 Planarity : 0.005 0.053 1312 Dihedral : 3.922 22.487 1028 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.07 % Allowed : 25.52 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.28), residues: 901 helix: 1.93 (0.21), residues: 546 sheet: -3.05 (0.85), residues: 17 loop : -0.57 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 1 89 TYR 0.012 0.001 TYR 1 698 PHE 0.010 0.001 PHE 1 275 TRP 0.012 0.001 TRP 1 167 HIS 0.008 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7660) covalent geometry : angle 0.59803 (10399) hydrogen bonds : bond 0.03707 ( 396) hydrogen bonds : angle 4.41145 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7723 (t0) REVERT: 1 185 ASP cc_start: 0.8892 (m-30) cc_final: 0.8577 (m-30) REVERT: 1 605 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: 1 766 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.8119 (p) REVERT: 1 948 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7930 (mm110) REVERT: 2 5 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6936 (tt) REVERT: 2 64 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.6815 (mmm160) REVERT: 2 80 ARG cc_start: 0.8726 (mtm180) cc_final: 0.8460 (ttm170) REVERT: 3 71 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6667 (mt-10) outliers start: 25 outliers final: 16 residues processed: 115 average time/residue: 0.5127 time to fit residues: 62.6388 Evaluate side-chains 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 241 LEU Chi-restraints excluded: chain 1 residue 243 ASP Chi-restraints excluded: chain 1 residue 262 ASN Chi-restraints excluded: chain 1 residue 369 ASN Chi-restraints excluded: chain 1 residue 420 VAL Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 664 ILE Chi-restraints excluded: chain 1 residue 688 MET Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 845 MET Chi-restraints excluded: chain 1 residue 867 SER Chi-restraints excluded: chain 1 residue 902 ILE Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 2 residue 64 ARG Chi-restraints excluded: chain 2 residue 112 VAL Chi-restraints excluded: chain 3 residue 62 THR Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 369 ASN 1 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086948 restraints weight = 12628.992| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.46 r_work: 0.3234 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7660 Z= 0.174 Angle : 0.625 14.417 10399 Z= 0.305 Chirality : 0.041 0.235 1187 Planarity : 0.005 0.054 1312 Dihedral : 4.027 24.439 1028 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.31 % Allowed : 24.79 % Favored : 71.90 % 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: 1.32 (0.28), residues: 901 helix: 1.88 (0.21), residues: 546 sheet: -2.91 (0.82), residues: 17 loop : -0.57 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 604 TYR 0.012 0.002 TYR 3 55 PHE 0.010 0.001 PHE 1 741 TRP 0.014 0.001 TRP 1 167 HIS 0.008 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7660) covalent geometry : angle 0.62541 (10399) hydrogen bonds : bond 0.03988 ( 396) hydrogen bonds : angle 4.52975 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7737 (t0) REVERT: 1 185 ASP cc_start: 0.8895 (m-30) cc_final: 0.8597 (m-30) REVERT: 1 393 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: 1 605 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: 1 607 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8179 (pp20) REVERT: 1 766 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8196 (p) REVERT: 1 948 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7920 (mm110) REVERT: 2 5 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6677 (tm) REVERT: 2 64 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.6845 (mmm160) REVERT: 2 77 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8523 (tt0) REVERT: 2 80 ARG cc_start: 0.8576 (mtm180) cc_final: 0.8279 (ttm170) REVERT: 3 71 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6664 (mt-10) outliers start: 27 outliers final: 15 residues processed: 117 average time/residue: 0.5797 time to fit residues: 71.8301 Evaluate side-chains 115 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 241 LEU Chi-restraints excluded: chain 1 residue 243 ASP Chi-restraints excluded: chain 1 residue 262 ASN Chi-restraints excluded: chain 1 residue 369 ASN Chi-restraints excluded: chain 1 residue 393 GLU Chi-restraints excluded: chain 1 residue 420 VAL Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 535 THR Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 607 GLU Chi-restraints excluded: chain 1 residue 664 ILE Chi-restraints excluded: chain 1 residue 688 MET Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 845 MET Chi-restraints excluded: chain 1 residue 867 SER Chi-restraints excluded: chain 1 residue 902 ILE Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 2 residue 64 ARG Chi-restraints excluded: chain 2 residue 112 VAL Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 0.0170 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 369 ASN 1 640 GLN 1 996 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.111502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089439 restraints weight = 12609.850| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.49 r_work: 0.3277 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7660 Z= 0.119 Angle : 0.603 13.435 10399 Z= 0.293 Chirality : 0.039 0.199 1187 Planarity : 0.005 0.055 1312 Dihedral : 3.937 23.478 1028 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.94 % Allowed : 26.01 % Favored : 71.04 % 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 aren not related in a simple way. whole: 1.42 (0.28), residues: 901 helix: 1.91 (0.21), residues: 552 sheet: -2.68 (0.83), residues: 17 loop : -0.50 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 1 89 TYR 0.012 0.001 TYR 1 698 PHE 0.011 0.001 PHE 1 275 TRP 0.013 0.001 TRP 1 167 HIS 0.010 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7660) covalent geometry : angle 0.60304 (10399) hydrogen bonds : bond 0.03620 ( 396) hydrogen bonds : angle 4.40705 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7686 (t0) REVERT: 1 185 ASP cc_start: 0.9044 (m-30) cc_final: 0.8721 (m-30) REVERT: 1 605 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: 1 607 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8170 (pp20) REVERT: 1 766 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8059 (p) REVERT: 1 951 GLU cc_start: 0.8353 (tp30) cc_final: 0.7893 (tp30) REVERT: 2 5 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6523 (tm) REVERT: 2 64 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.6808 (mmm160) REVERT: 2 77 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8464 (tt0) REVERT: 2 80 ARG cc_start: 0.8548 (mtm180) cc_final: 0.8268 (ttm170) REVERT: 3 71 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6673 (mt-10) outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 0.5078 time to fit residues: 59.8221 Evaluate side-chains 110 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 241 LEU Chi-restraints excluded: chain 1 residue 243 ASP Chi-restraints excluded: chain 1 residue 262 ASN Chi-restraints excluded: chain 1 residue 420 VAL Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 535 THR Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 607 GLU Chi-restraints excluded: chain 1 residue 664 ILE Chi-restraints excluded: chain 1 residue 688 MET Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 845 MET Chi-restraints excluded: chain 1 residue 867 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 2 residue 64 ARG Chi-restraints excluded: chain 3 residue 62 THR Chi-restraints excluded: chain 3 residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 75 optimal weight: 0.0060 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 640 GLN ** 1 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.110552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088401 restraints weight = 12454.277| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.47 r_work: 0.3261 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7660 Z= 0.137 Angle : 0.602 13.159 10399 Z= 0.294 Chirality : 0.039 0.200 1187 Planarity : 0.005 0.052 1312 Dihedral : 3.926 22.535 1028 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.58 % Allowed : 26.50 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.28), residues: 901 helix: 1.92 (0.21), residues: 552 sheet: -2.42 (0.87), residues: 17 loop : -0.49 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 1 89 TYR 0.012 0.001 TYR 1 698 PHE 0.011 0.001 PHE 1 275 TRP 0.013 0.001 TRP 1 167 HIS 0.009 0.001 HIS 1 441 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7660) covalent geometry : angle 0.60176 (10399) hydrogen bonds : bond 0.03743 ( 396) hydrogen bonds : angle 4.44593 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3509.05 seconds wall clock time: 60 minutes 21.89 seconds (3621.89 seconds total)