Starting phenix.real_space_refine on Tue Jan 14 22:15:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f3f_50173/01_2025/9f3f_50173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f3f_50173/01_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_50173/01_2025/9f3f_50173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f3f_50173/01_2025/9f3f_50173.map" model { file = "/net/cci-nas-00/data/ceres_data/9f3f_50173/01_2025/9f3f_50173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f3f_50173/01_2025/9f3f_50173.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.45, per 1000 atoms: 0.73 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: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.79 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: 2.27 Time building geometry restraints manager: 2.32 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- 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= 0.508 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 : 16.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.047 0.003 TRP 1 111 HIS 0.009 0.001 HIS 1 163 PHE 0.023 0.002 PHE 1 51 TYR 0.028 0.003 TYR 2 4 ARG 0.012 0.001 ARG 1 526 *********************** 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 : 0.852 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: 1.2924 time to fit residues: 245.6279 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 : 0.935 ------------------------------------------------------------------------------- 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 78 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.111983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090029 restraints weight = 12340.558| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.44 r_work: 0.3282 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7660 Z= 0.250 Angle : 0.629 7.884 10399 Z= 0.323 Chirality : 0.040 0.220 1187 Planarity : 0.005 0.057 1312 Dihedral : 4.323 25.741 1031 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.42 % Allowed : 22.09 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.28), residues: 901 helix: 1.33 (0.21), residues: 560 sheet: -3.70 (0.95), residues: 10 loop : -0.77 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 1 57 HIS 0.007 0.001 HIS 1 441 PHE 0.008 0.001 PHE 1 776 TYR 0.021 0.002 TYR 2 4 ARG 0.009 0.001 ARG 1 440 *********************** 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: 36 poor density : 107 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: 1 216 GLU cc_start: 0.8124 (tp30) cc_final: 0.7699 (tp30) REVERT: 1 393 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: 1 605 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7985 (mt-10) REVERT: 1 688 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8020 (tpp) REVERT: 1 766 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8169 (p) REVERT: 1 948 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7865 (mm110) REVERT: 2 80 ARG cc_start: 0.8669 (mtm180) cc_final: 0.8427 (ttm170) REVERT: 3 69 GLU cc_start: 0.8623 (tp30) cc_final: 0.8244 (tp30) REVERT: 3 71 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6249 (mt-10) outliers start: 36 outliers final: 5 residues processed: 131 average time/residue: 1.3129 time to fit residues: 182.8174 Evaluate side-chains 102 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 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 50 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 0.0370 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.112019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090081 restraints weight = 12430.635| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.44 r_work: 0.3285 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7660 Z= 0.207 Angle : 0.570 7.596 10399 Z= 0.289 Chirality : 0.039 0.140 1187 Planarity : 0.005 0.053 1312 Dihedral : 4.103 23.721 1029 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.66 % Allowed : 21.60 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.28), residues: 901 helix: 1.67 (0.22), residues: 553 sheet: -3.32 (0.90), residues: 17 loop : -0.52 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 57 HIS 0.007 0.001 HIS 1 441 PHE 0.009 0.001 PHE 1 776 TYR 0.015 0.001 TYR 2 4 ARG 0.007 0.001 ARG 1 563 *********************** 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 144 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7862 (t0) REVERT: 1 191 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7257 (pp30) REVERT: 1 216 GLU cc_start: 0.8091 (tp30) cc_final: 0.7859 (tp30) REVERT: 1 393 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: 1 605 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7957 (mt-10) REVERT: 1 766 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8173 (p) REVERT: 1 948 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7872 (mm110) REVERT: 2 5 LEU cc_start: 0.8161 (tt) cc_final: 0.7744 (tt) REVERT: 2 33 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7769 (ttp80) REVERT: 2 64 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.6819 (mmm160) REVERT: 2 80 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8309 (ttm170) REVERT: 3 71 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6479 (mt-10) outliers start: 38 outliers final: 9 residues processed: 135 average time/residue: 1.1986 time to fit residues: 171.5882 Evaluate side-chains 107 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 191 GLN Chi-restraints excluded: chain 1 residue 241 LEU Chi-restraints excluded: chain 1 residue 278 VAL 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 766 SER 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 31 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** 1 640 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 = 0.3759 r_free = 0.3759 target = 0.109567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087320 restraints weight = 12580.779| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.47 r_work: 0.3239 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7660 Z= 0.285 Angle : 0.583 6.296 10399 Z= 0.298 Chirality : 0.041 0.225 1187 Planarity : 0.005 0.054 1312 Dihedral : 4.163 24.560 1029 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.17 % Allowed : 22.21 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 901 helix: 1.67 (0.22), residues: 548 sheet: -3.25 (0.90), residues: 17 loop : -0.53 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 57 HIS 0.007 0.001 HIS 1 441 PHE 0.017 0.002 PHE 2 30 TYR 0.014 0.002 TYR 3 55 ARG 0.006 0.000 ARG 1 563 *********************** 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 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7802 (t0) REVERT: 1 188 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: 1 216 GLU cc_start: 0.8218 (tp30) cc_final: 0.7862 (tp30) REVERT: 1 393 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: 1 664 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8719 (pp) REVERT: 1 766 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8193 (p) REVERT: 1 948 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7855 (mm110) REVERT: 2 5 LEU cc_start: 0.7897 (tt) cc_final: 0.7469 (tt) REVERT: 2 55 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8664 (mt-10) REVERT: 2 64 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.6836 (mmm160) REVERT: 2 80 ARG cc_start: 0.8641 (mtm180) cc_final: 0.8416 (ttm170) REVERT: 3 71 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6596 (mt-10) outliers start: 34 outliers final: 10 residues processed: 125 average time/residue: 1.1645 time to fit residues: 155.3280 Evaluate side-chains 112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 97 LYS Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 188 GLU Chi-restraints excluded: chain 1 residue 243 ASP Chi-restraints excluded: chain 1 residue 393 GLU Chi-restraints excluded: chain 1 residue 436 SER 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 766 SER 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 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 191 GLN 1 640 GLN 2 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088047 restraints weight = 12395.954| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.47 r_work: 0.3254 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7660 Z= 0.226 Angle : 0.573 13.898 10399 Z= 0.286 Chirality : 0.039 0.154 1187 Planarity : 0.005 0.055 1312 Dihedral : 4.014 25.906 1028 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.93 % Allowed : 22.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 901 helix: 1.73 (0.21), residues: 547 sheet: -3.45 (0.87), residues: 17 loop : -0.48 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 57 HIS 0.008 0.001 HIS 1 441 PHE 0.010 0.001 PHE 2 30 TYR 0.012 0.001 TYR 3 55 ARG 0.005 0.000 ARG 1 604 *********************** 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 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7769 (t0) REVERT: 1 191 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7510 (pp30) REVERT: 1 216 GLU cc_start: 0.8208 (tp30) cc_final: 0.7761 (tp30) REVERT: 1 393 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: 1 664 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8710 (pp) REVERT: 1 688 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8019 (tpp) REVERT: 1 766 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8136 (p) REVERT: 1 948 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7898 (mm110) REVERT: 2 5 LEU cc_start: 0.7691 (tt) cc_final: 0.7173 (tt) REVERT: 2 33 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8027 (ttp80) REVERT: 2 39 ASN cc_start: 0.8324 (m110) cc_final: 0.8108 (m-40) REVERT: 2 80 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8302 (ttm170) REVERT: 3 71 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6591 (mt-10) outliers start: 32 outliers final: 11 residues processed: 123 average time/residue: 1.1145 time to fit residues: 146.1747 Evaluate side-chains 111 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 97 LYS Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 191 GLN 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 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 867 SER Chi-restraints excluded: chain 1 residue 954 LEU 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 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.110078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087945 restraints weight = 12583.522| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.47 r_work: 0.3250 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7660 Z= 0.223 Angle : 0.578 10.619 10399 Z= 0.293 Chirality : 0.039 0.151 1187 Planarity : 0.005 0.053 1312 Dihedral : 3.975 24.436 1028 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.80 % Allowed : 22.70 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 901 helix: 1.75 (0.21), residues: 548 sheet: -3.37 (0.86), residues: 17 loop : -0.48 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 57 HIS 0.008 0.001 HIS 1 441 PHE 0.014 0.001 PHE 1 275 TYR 0.012 0.001 TYR 1 698 ARG 0.004 0.000 ARG 1 604 *********************** 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: 31 poor density : 99 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: 1 115 CYS cc_start: 0.8724 (t) cc_final: 0.8450 (m) REVERT: 1 120 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7794 (t0) REVERT: 1 216 GLU cc_start: 0.8202 (tp30) cc_final: 0.7994 (tp30) REVERT: 1 393 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: 1 605 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: 1 766 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8137 (p) REVERT: 1 948 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7897 (mm110) REVERT: 2 5 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7039 (tt) REVERT: 2 33 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8038 (ttp80) REVERT: 2 39 ASN cc_start: 0.8336 (m110) cc_final: 0.8125 (m-40) REVERT: 2 80 ARG cc_start: 0.8644 (mtm180) cc_final: 0.8371 (ttm170) REVERT: 3 71 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6671 (mt-10) outliers start: 31 outliers final: 14 residues processed: 119 average time/residue: 1.1177 time to fit residues: 142.0286 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 TYR Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 97 LYS 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 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 664 ILE Chi-restraints excluded: chain 1 residue 766 SER Chi-restraints excluded: chain 1 residue 845 MET 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 56 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 191 GLN 1 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.111044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089066 restraints weight = 12413.633| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.47 r_work: 0.3271 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7660 Z= 0.194 Angle : 0.558 9.242 10399 Z= 0.279 Chirality : 0.038 0.121 1187 Planarity : 0.004 0.054 1312 Dihedral : 3.897 24.132 1028 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.31 % Allowed : 23.80 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 901 helix: 1.79 (0.21), residues: 554 sheet: -3.27 (0.88), residues: 17 loop : -0.43 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 57 HIS 0.008 0.001 HIS 1 441 PHE 0.014 0.001 PHE 1 275 TYR 0.012 0.001 TYR 1 698 ARG 0.008 0.000 ARG 1 89 *********************** 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 131 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7773 (t0) REVERT: 1 191 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7596 (pp30) REVERT: 1 216 GLU cc_start: 0.8147 (tp30) cc_final: 0.7927 (tp30) REVERT: 1 766 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8096 (p) REVERT: 1 855 SER cc_start: 0.9073 (t) cc_final: 0.8658 (p) REVERT: 1 948 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7928 (mm110) REVERT: 2 5 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6942 (tt) REVERT: 2 33 ARG cc_start: 0.8364 (ttp80) cc_final: 0.8044 (ttp80) REVERT: 2 80 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8348 (ttm170) REVERT: 3 71 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6641 (mt-10) outliers start: 27 outliers final: 15 residues processed: 122 average time/residue: 1.1913 time to fit residues: 154.6246 Evaluate side-chains 121 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 TYR Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 97 LYS Chi-restraints excluded: chain 1 residue 120 ASP Chi-restraints excluded: chain 1 residue 191 GLN Chi-restraints excluded: chain 1 residue 241 LEU 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 535 THR Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 664 ILE 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 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 64 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.110261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088238 restraints weight = 12616.007| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.48 r_work: 0.3255 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3006 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= 0.219 Angle : 0.569 11.742 10399 Z= 0.282 Chirality : 0.040 0.278 1187 Planarity : 0.005 0.052 1312 Dihedral : 3.895 23.684 1028 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.68 % Allowed : 23.80 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.28), residues: 901 helix: 1.83 (0.21), residues: 552 sheet: -3.21 (0.89), residues: 17 loop : -0.44 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 390 HIS 0.008 0.001 HIS 1 441 PHE 0.010 0.001 PHE 1 275 TYR 0.011 0.001 TYR 1 698 ARG 0.006 0.000 ARG 1 89 *********************** 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 129 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7810 (t0) REVERT: 1 216 GLU cc_start: 0.8158 (tp30) cc_final: 0.7956 (tp30) REVERT: 1 605 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: 1 766 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8107 (p) REVERT: 1 855 SER cc_start: 0.9083 (t) cc_final: 0.8668 (p) REVERT: 1 948 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7930 (mm110) REVERT: 2 5 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6715 (tm) REVERT: 2 33 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8064 (ttp80) REVERT: 2 80 ARG cc_start: 0.8653 (mtm180) cc_final: 0.8396 (ttm170) REVERT: 3 71 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6641 (mt-10) outliers start: 30 outliers final: 18 residues processed: 119 average time/residue: 1.1427 time to fit residues: 144.9618 Evaluate side-chains 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 TYR Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 97 LYS 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 369 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 577 LEU Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 664 ILE 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 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 50 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.111172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088985 restraints weight = 12731.515| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.51 r_work: 0.3266 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3037 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= 0.196 Angle : 0.579 11.081 10399 Z= 0.286 Chirality : 0.039 0.219 1187 Planarity : 0.004 0.053 1312 Dihedral : 3.883 23.894 1028 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.07 % Allowed : 24.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.28), residues: 901 helix: 1.86 (0.21), residues: 553 sheet: -3.05 (0.92), residues: 17 loop : -0.40 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 57 HIS 0.009 0.001 HIS 1 441 PHE 0.009 0.001 PHE 1 741 TYR 0.012 0.001 TYR 1 698 ARG 0.006 0.000 ARG 1 604 *********************** 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 123 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.913 Fit side-chains REVERT: 1 120 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7776 (t0) REVERT: 1 216 GLU cc_start: 0.8158 (tp30) cc_final: 0.7684 (tp30) REVERT: 1 393 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: 1 605 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: 1 766 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8085 (p) REVERT: 1 951 GLU cc_start: 0.8306 (tp30) cc_final: 0.7845 (tp30) REVERT: 2 1 MET cc_start: 0.5559 (OUTLIER) cc_final: 0.5248 (pp-130) REVERT: 2 5 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6729 (tm) REVERT: 2 33 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8069 (ttp80) REVERT: 2 80 ARG cc_start: 0.8645 (mtm180) cc_final: 0.8384 (ttm170) REVERT: 3 71 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6598 (mt-10) outliers start: 25 outliers final: 14 residues processed: 113 average time/residue: 1.1783 time to fit residues: 142.0245 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 TYR Chi-restraints excluded: chain 1 residue 97 LYS Chi-restraints excluded: chain 1 residue 120 ASP 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 535 THR Chi-restraints excluded: chain 1 residue 577 LEU Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 664 ILE 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 2 residue 1 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 192 ASN 1 640 GLN ** 1 948 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 = 0.3783 r_free = 0.3783 target = 0.110836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088699 restraints weight = 12693.660| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.50 r_work: 0.3262 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3070 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= 0.198 Angle : 0.567 10.828 10399 Z= 0.280 Chirality : 0.039 0.212 1187 Planarity : 0.004 0.052 1312 Dihedral : 3.856 23.016 1028 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.82 % Allowed : 25.15 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 901 helix: 1.89 (0.21), residues: 553 sheet: -3.01 (0.85), residues: 17 loop : -0.39 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 111 HIS 0.009 0.001 HIS 1 441 PHE 0.009 0.001 PHE 1 741 TYR 0.012 0.001 TYR 1 698 ARG 0.006 0.000 ARG 1 89 ********************** 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: 23 poor density : 97 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: 1 120 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7750 (t0) REVERT: 1 192 ASN cc_start: 0.7480 (m-40) cc_final: 0.6072 (m-40) REVERT: 1 216 GLU cc_start: 0.8147 (tp30) cc_final: 0.7883 (tp30) REVERT: 1 605 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: 1 766 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8059 (p) REVERT: 1 948 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7796 (mm110) REVERT: 2 1 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.5240 (pp-130) REVERT: 2 5 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6729 (tm) REVERT: 2 80 ARG cc_start: 0.8653 (mtm180) cc_final: 0.8394 (ttm170) REVERT: 3 71 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6617 (mt-10) outliers start: 23 outliers final: 15 residues processed: 110 average time/residue: 1.1924 time to fit residues: 139.4822 Evaluate side-chains 112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 TYR Chi-restraints excluded: chain 1 residue 97 LYS Chi-restraints excluded: chain 1 residue 120 ASP 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 420 VAL Chi-restraints excluded: chain 1 residue 436 SER Chi-restraints excluded: chain 1 residue 535 THR Chi-restraints excluded: chain 1 residue 577 LEU Chi-restraints excluded: chain 1 residue 605 GLU Chi-restraints excluded: chain 1 residue 664 ILE 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 2 residue 1 MET Chi-restraints excluded: chain 2 residue 5 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 640 GLN ** 1 948 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 = 0.3782 r_free = 0.3782 target = 0.110781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088617 restraints weight = 12528.929| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.48 r_work: 0.3263 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3111 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= 0.207 Angle : 0.587 12.334 10399 Z= 0.292 Chirality : 0.039 0.201 1187 Planarity : 0.005 0.053 1312 Dihedral : 3.881 23.799 1028 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.07 % Allowed : 25.28 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.28), residues: 901 helix: 1.90 (0.21), residues: 554 sheet: -2.95 (0.83), residues: 17 loop : -0.38 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 111 HIS 0.009 0.001 HIS 1 441 PHE 0.009 0.001 PHE 1 741 TYR 0.012 0.001 TYR 1 698 ARG 0.006 0.000 ARG 1 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7177.74 seconds wall clock time: 127 minutes 40.42 seconds (7660.42 seconds total)