Starting phenix.real_space_refine on Tue Feb 11 22:53:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9euq_19980/02_2025/9euq_19980.cif Found real_map, /net/cci-nas-00/data/ceres_data/9euq_19980/02_2025/9euq_19980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9euq_19980/02_2025/9euq_19980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9euq_19980/02_2025/9euq_19980.map" model { file = "/net/cci-nas-00/data/ceres_data/9euq_19980/02_2025/9euq_19980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9euq_19980/02_2025/9euq_19980.cif" } resolution = 2.98 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= 0.013 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 33 5.16 5 Be 1 3.05 5 C 4269 2.51 5 N 1110 2.21 5 O 1276 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6693 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6688 Classifications: {'peptide': 880} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 29, 'TRANS': 850} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.52, per 1000 atoms: 0.82 Number of scatterers: 6693 At special positions: 0 Unit cell: (69.696, 91.52, 128.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 33 16.00 Mg 1 11.99 F 3 9.00 O 1276 8.00 N 1110 7.00 C 4269 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 56.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 57 through 74 Processing helix chain 'A' and resid 75 through 102 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.892A pdb=" N ARG A 187 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 230 through 264 Processing helix chain 'A' and resid 270 through 290 Processing helix chain 'A' and resid 293 through 311 Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.567A pdb=" N GLU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.570A pdb=" N VAL A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.834A pdb=" N ILE A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 472 through 488 Processing helix chain 'A' and resid 528 through 541 removed outlier: 4.026A pdb=" N TYR A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 563 Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.339A pdb=" N ALA A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'A' and resid 660 through 701 removed outlier: 4.031A pdb=" N VAL A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 752 through 777 Processing helix chain 'A' and resid 779 through 802 removed outlier: 4.151A pdb=" N THR A 799 " --> pdb=" O ARG A 795 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 817 through 835 Processing helix chain 'A' and resid 850 through 879 Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 127 removed outlier: 4.273A pdb=" N LYS A 116 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL A 136 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 196 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 158 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 200 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N SER A 156 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 202 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 154 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 204 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 152 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 206 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG A 150 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 157 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 127 removed outlier: 4.273A pdb=" N LYS A 116 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL A 136 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 196 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 158 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 200 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N SER A 156 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 202 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 154 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 204 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 152 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 206 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG A 150 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 removed outlier: 6.596A pdb=" N GLY A 637 " --> pdb=" O MET A 653 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU A 655 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 639 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N MET A 620 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET A 640 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 333 removed outlier: 6.226A pdb=" N ILE A 331 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE A 548 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR A 333 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR A 596 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET A 547 " --> pdb=" O TYR A 596 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 350 removed outlier: 4.179A pdb=" N GLY A 519 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 496 " --> pdb=" O THR A 447 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1167 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: 2.49 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2205 1.34 - 1.46: 1369 1.46 - 1.58: 3154 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 6789 Sorted by residual: bond pdb=" N VAL A 516 " pdb=" CA VAL A 516 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.61e+00 bond pdb=" N ILE A 515 " pdb=" CA ILE A 515 " ideal model delta sigma weight residual 1.460 1.496 -0.035 1.30e-02 5.92e+03 7.39e+00 bond pdb=" N PHE A 843 " pdb=" CA PHE A 843 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.10e-02 8.26e+03 7.16e+00 bond pdb=" N GLU A 167 " pdb=" CA GLU A 167 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.96e+00 bond pdb=" N LEU A 478 " pdb=" CA LEU A 478 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.35e+00 ... (remaining 6784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 9070 2.28 - 4.57: 97 4.57 - 6.85: 14 6.85 - 9.14: 4 9.14 - 11.42: 1 Bond angle restraints: 9186 Sorted by residual: angle pdb=" CB MET A 782 " pdb=" CG MET A 782 " pdb=" SD MET A 782 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA LYS A 356 " pdb=" CB LYS A 356 " pdb=" CG LYS A 356 " ideal model delta sigma weight residual 114.10 121.57 -7.47 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C LEU A 104 " pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 121.54 128.46 -6.92 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N ILE A 515 " pdb=" CA ILE A 515 " pdb=" C ILE A 515 " ideal model delta sigma weight residual 113.22 109.00 4.22 1.23e+00 6.61e-01 1.18e+01 angle pdb=" C LYS A 43 " pdb=" N LYS A 44 " pdb=" CA LYS A 44 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 ... (remaining 9181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3504 17.88 - 35.76: 467 35.76 - 53.63: 120 53.63 - 71.51: 36 71.51 - 89.39: 9 Dihedral angle restraints: 4136 sinusoidal: 1609 harmonic: 2527 Sorted by residual: dihedral pdb=" CA ASP A 135 " pdb=" CB ASP A 135 " pdb=" CG ASP A 135 " pdb=" OD1 ASP A 135 " ideal model delta sinusoidal sigma weight residual -30.00 -83.49 53.49 1 2.00e+01 2.50e-03 9.72e+00 dihedral pdb=" CB LYS A 540 " pdb=" CG LYS A 540 " pdb=" CD LYS A 540 " pdb=" CE LYS A 540 " ideal model delta sinusoidal sigma weight residual -180.00 -120.61 -59.39 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLU A 583 " pdb=" CA GLU A 583 " pdb=" CB GLU A 583 " pdb=" CG GLU A 583 " ideal model delta sinusoidal sigma weight residual -60.00 -119.26 59.26 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 736 0.034 - 0.068: 250 0.068 - 0.102: 81 0.102 - 0.136: 25 0.136 - 0.170: 7 Chirality restraints: 1099 Sorted by residual: chirality pdb=" CA GLU A 167 " pdb=" N GLU A 167 " pdb=" C GLU A 167 " pdb=" CB GLU A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CB ILE A 401 " pdb=" CA ILE A 401 " pdb=" CG1 ILE A 401 " pdb=" CG2 ILE A 401 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CG LEU A 379 " pdb=" CB LEU A 379 " pdb=" CD1 LEU A 379 " pdb=" CD2 LEU A 379 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 1096 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 132 " 0.026 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 133 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 843 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C PHE A 843 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A 843 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 844 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 230 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 231 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.018 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 94 2.60 - 3.18: 5973 3.18 - 3.75: 11733 3.75 - 4.33: 15139 4.33 - 4.90: 25419 Nonbonded interactions: 58358 Sorted by model distance: nonbonded pdb=" OD2 ASP A 334 " pdb="MG MG A 901 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP A 623 " pdb="MG MG A 901 " model vdw 2.060 2.170 nonbonded pdb=" O THR A 336 " pdb="MG MG A 901 " model vdw 2.109 2.170 nonbonded pdb=" O ARG A 108 " pdb=" OG SER A 111 " model vdw 2.209 3.040 nonbonded pdb=" O LEU A 236 " pdb=" OG SER A 240 " model vdw 2.222 3.040 ... (remaining 58353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.290 Find NCS groups from input model: 0.070 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6789 Z= 0.177 Angle : 0.581 11.422 9186 Z= 0.304 Chirality : 0.041 0.170 1099 Planarity : 0.003 0.045 1174 Dihedral : 18.086 89.391 2504 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.56 % Allowed : 36.73 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.29), residues: 878 helix: 1.63 (0.24), residues: 487 sheet: -0.65 (0.61), residues: 75 loop : -1.27 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 703 HIS 0.001 0.000 HIS A 592 PHE 0.007 0.001 PHE A 843 TYR 0.013 0.001 TYR A 831 ARG 0.009 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8420 (ptm) cc_final: 0.8120 (ttp) REVERT: A 226 GLU cc_start: 0.7430 (tt0) cc_final: 0.6834 (tt0) REVERT: A 271 MET cc_start: 0.7004 (tpt) cc_final: 0.4723 (pmm) REVERT: A 292 GLU cc_start: 0.8475 (mp0) cc_final: 0.8005 (mp0) REVERT: A 462 PHE cc_start: 0.8124 (t80) cc_final: 0.7902 (t80) REVERT: A 480 GLU cc_start: 0.8929 (tt0) cc_final: 0.8601 (tp30) REVERT: A 487 ASN cc_start: 0.8387 (m-40) cc_final: 0.7490 (t0) outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 1.0134 time to fit residues: 121.9624 Evaluate side-chains 97 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 707 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.164803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119835 restraints weight = 8153.770| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.99 r_work: 0.3391 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6789 Z= 0.252 Angle : 0.572 7.572 9186 Z= 0.288 Chirality : 0.042 0.137 1099 Planarity : 0.004 0.048 1174 Dihedral : 4.152 36.498 931 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.28 % Allowed : 30.31 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.29), residues: 878 helix: 1.58 (0.23), residues: 484 sheet: -0.82 (0.61), residues: 81 loop : -1.36 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 48 HIS 0.002 0.000 HIS A 437 PHE 0.009 0.001 PHE A 685 TYR 0.016 0.001 TYR A 831 ARG 0.004 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.8439 (ptm) cc_final: 0.8153 (ttp) REVERT: A 226 GLU cc_start: 0.7429 (tt0) cc_final: 0.6806 (tt0) REVERT: A 271 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.4856 (pmm) REVERT: A 292 GLU cc_start: 0.8635 (mp0) cc_final: 0.8087 (mp0) REVERT: A 375 HIS cc_start: 0.8390 (m-70) cc_final: 0.8189 (m90) REVERT: A 462 PHE cc_start: 0.7865 (t80) cc_final: 0.7595 (t80) REVERT: A 480 GLU cc_start: 0.8927 (tt0) cc_final: 0.8604 (tp30) REVERT: A 484 GLU cc_start: 0.7956 (tp30) cc_final: 0.7258 (tp30) REVERT: A 487 ASN cc_start: 0.8419 (m-40) cc_final: 0.7527 (t0) REVERT: A 613 LYS cc_start: 0.8603 (tttm) cc_final: 0.8374 (ttpp) REVERT: A 640 MET cc_start: 0.8931 (mmm) cc_final: 0.8285 (mmt) REVERT: A 729 MET cc_start: 0.8866 (mmp) cc_final: 0.8643 (mmt) outliers start: 45 outliers final: 16 residues processed: 137 average time/residue: 0.8920 time to fit residues: 131.5132 Evaluate side-chains 112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.164423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118848 restraints weight = 8292.687| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.02 r_work: 0.3364 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6789 Z= 0.270 Angle : 0.573 8.747 9186 Z= 0.285 Chirality : 0.043 0.183 1099 Planarity : 0.004 0.050 1174 Dihedral : 3.975 22.390 929 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.45 % Allowed : 32.12 % Favored : 62.43 % 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: 0.43 (0.28), residues: 878 helix: 1.51 (0.23), residues: 484 sheet: -0.75 (0.67), residues: 65 loop : -1.38 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 703 HIS 0.001 0.001 HIS A 552 PHE 0.010 0.001 PHE A 674 TYR 0.014 0.001 TYR A 831 ARG 0.004 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7654 (tt) REVERT: A 226 GLU cc_start: 0.7473 (tt0) cc_final: 0.6847 (tt0) REVERT: A 292 GLU cc_start: 0.8644 (mp0) cc_final: 0.8212 (mp0) REVERT: A 375 HIS cc_start: 0.8403 (m-70) cc_final: 0.8175 (m90) REVERT: A 462 PHE cc_start: 0.7889 (t80) cc_final: 0.7654 (t80) REVERT: A 484 GLU cc_start: 0.7975 (tp30) cc_final: 0.7304 (tp30) REVERT: A 487 ASN cc_start: 0.8453 (m-40) cc_final: 0.7595 (t0) REVERT: A 523 MET cc_start: 0.8789 (ttm) cc_final: 0.8533 (mtm) REVERT: A 613 LYS cc_start: 0.8668 (tttm) cc_final: 0.8444 (ttpp) REVERT: A 804 SER cc_start: 0.8586 (m) cc_final: 0.8310 (t) outliers start: 39 outliers final: 19 residues processed: 129 average time/residue: 0.8737 time to fit residues: 121.1269 Evaluate side-chains 114 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.0040 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120683 restraints weight = 8360.801| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.01 r_work: 0.3398 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6789 Z= 0.203 Angle : 0.555 9.450 9186 Z= 0.275 Chirality : 0.042 0.183 1099 Planarity : 0.004 0.049 1174 Dihedral : 3.916 21.972 929 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.15 % Allowed : 32.68 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.29), residues: 878 helix: 1.68 (0.23), residues: 483 sheet: -0.71 (0.68), residues: 65 loop : -1.37 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 703 HIS 0.001 0.000 HIS A 552 PHE 0.008 0.001 PHE A 685 TYR 0.013 0.001 TYR A 831 ARG 0.007 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8131 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 163 MET cc_start: 0.8479 (ptm) cc_final: 0.8270 (ttp) REVERT: A 189 ASN cc_start: 0.9074 (p0) cc_final: 0.8801 (p0) REVERT: A 196 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 226 GLU cc_start: 0.7419 (tt0) cc_final: 0.6868 (tt0) REVERT: A 292 GLU cc_start: 0.8564 (mp0) cc_final: 0.8056 (mp0) REVERT: A 375 HIS cc_start: 0.8402 (m-70) cc_final: 0.8128 (m90) REVERT: A 462 PHE cc_start: 0.7822 (t80) cc_final: 0.7575 (t80) REVERT: A 480 GLU cc_start: 0.8932 (tt0) cc_final: 0.8617 (tp30) REVERT: A 484 GLU cc_start: 0.7979 (tp30) cc_final: 0.7312 (tp30) REVERT: A 487 ASN cc_start: 0.8423 (m-40) cc_final: 0.7547 (t0) REVERT: A 523 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8439 (mtm) REVERT: A 583 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: A 620 MET cc_start: 0.9152 (tpt) cc_final: 0.8771 (tpt) outliers start: 44 outliers final: 17 residues processed: 140 average time/residue: 0.8543 time to fit residues: 128.6112 Evaluate side-chains 119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.164675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120202 restraints weight = 8320.907| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.99 r_work: 0.3406 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6789 Z= 0.227 Angle : 0.596 11.686 9186 Z= 0.288 Chirality : 0.042 0.182 1099 Planarity : 0.004 0.051 1174 Dihedral : 3.921 22.033 929 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.59 % Allowed : 33.38 % Favored : 61.03 % 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: 0.51 (0.28), residues: 878 helix: 1.63 (0.23), residues: 483 sheet: -0.95 (0.67), residues: 65 loop : -1.36 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.001 0.000 HIS A 552 PHE 0.008 0.001 PHE A 685 TYR 0.014 0.002 TYR A 349 ARG 0.009 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8628 (tptt) REVERT: A 153 GLU cc_start: 0.8109 (tt0) cc_final: 0.7317 (tm-30) REVERT: A 167 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: A 189 ASN cc_start: 0.9082 (p0) cc_final: 0.8769 (p0) REVERT: A 196 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7602 (tt) REVERT: A 226 GLU cc_start: 0.7391 (tt0) cc_final: 0.6833 (tt0) REVERT: A 234 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7466 (ttm-80) REVERT: A 292 GLU cc_start: 0.8600 (mp0) cc_final: 0.8276 (mp0) REVERT: A 375 HIS cc_start: 0.8364 (m-70) cc_final: 0.8092 (m90) REVERT: A 462 PHE cc_start: 0.7728 (t80) cc_final: 0.7440 (t80) REVERT: A 480 GLU cc_start: 0.8915 (tt0) cc_final: 0.8598 (tp30) REVERT: A 484 GLU cc_start: 0.7981 (tp30) cc_final: 0.7291 (tp30) REVERT: A 487 ASN cc_start: 0.8410 (m-40) cc_final: 0.7549 (t0) REVERT: A 523 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8425 (mtm) outliers start: 40 outliers final: 18 residues processed: 135 average time/residue: 0.8805 time to fit residues: 127.6482 Evaluate side-chains 122 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 74 optimal weight: 0.0770 chunk 76 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.165993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121873 restraints weight = 8359.134| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.99 r_work: 0.3412 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6789 Z= 0.203 Angle : 0.585 11.222 9186 Z= 0.283 Chirality : 0.042 0.188 1099 Planarity : 0.004 0.052 1174 Dihedral : 3.884 22.894 929 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.01 % Allowed : 33.10 % Favored : 60.89 % 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: 0.62 (0.29), residues: 878 helix: 1.72 (0.23), residues: 483 sheet: -0.98 (0.67), residues: 65 loop : -1.31 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.001 0.000 HIS A 375 PHE 0.009 0.001 PHE A 455 TYR 0.013 0.001 TYR A 831 ARG 0.009 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8646 (tptt) REVERT: A 153 GLU cc_start: 0.8110 (tt0) cc_final: 0.7351 (tm-30) REVERT: A 167 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: A 189 ASN cc_start: 0.9072 (p0) cc_final: 0.8770 (p0) REVERT: A 196 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7592 (tt) REVERT: A 226 GLU cc_start: 0.7372 (tt0) cc_final: 0.6814 (tt0) REVERT: A 292 GLU cc_start: 0.8560 (mp0) cc_final: 0.8221 (mp0) REVERT: A 375 HIS cc_start: 0.8355 (m-70) cc_final: 0.8091 (m90) REVERT: A 460 TYR cc_start: 0.7197 (m-80) cc_final: 0.6985 (m-80) REVERT: A 462 PHE cc_start: 0.7776 (t80) cc_final: 0.7392 (t80) REVERT: A 480 GLU cc_start: 0.8910 (tt0) cc_final: 0.8591 (tp30) REVERT: A 484 GLU cc_start: 0.7972 (tp30) cc_final: 0.7258 (tp30) REVERT: A 487 ASN cc_start: 0.8387 (m-40) cc_final: 0.7533 (t0) REVERT: A 497 TYR cc_start: 0.7713 (p90) cc_final: 0.7286 (p90) REVERT: A 523 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8403 (mtm) REVERT: A 583 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: A 880 LYS cc_start: 0.5495 (OUTLIER) cc_final: 0.3702 (tptt) outliers start: 43 outliers final: 16 residues processed: 133 average time/residue: 0.8571 time to fit residues: 123.2618 Evaluate side-chains 121 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119074 restraints weight = 8325.179| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.00 r_work: 0.3383 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6789 Z= 0.261 Angle : 0.618 11.181 9186 Z= 0.297 Chirality : 0.043 0.172 1099 Planarity : 0.004 0.053 1174 Dihedral : 3.942 22.917 929 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.87 % Allowed : 33.66 % Favored : 60.47 % 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: 0.53 (0.28), residues: 878 helix: 1.63 (0.23), residues: 483 sheet: -0.99 (0.68), residues: 63 loop : -1.33 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 703 HIS 0.001 0.000 HIS A 592 PHE 0.009 0.001 PHE A 239 TYR 0.014 0.002 TYR A 831 ARG 0.011 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.734 Fit side-chains REVERT: A 2 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: A 29 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8619 (tptt) REVERT: A 48 TRP cc_start: 0.8056 (p-90) cc_final: 0.7798 (p-90) REVERT: A 153 GLU cc_start: 0.8124 (tt0) cc_final: 0.7354 (tm-30) REVERT: A 167 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: A 189 ASN cc_start: 0.9079 (p0) cc_final: 0.8765 (p0) REVERT: A 196 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7649 (tt) REVERT: A 226 GLU cc_start: 0.7420 (tt0) cc_final: 0.6868 (tt0) REVERT: A 234 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7550 (ttm-80) REVERT: A 292 GLU cc_start: 0.8618 (mp0) cc_final: 0.8197 (mp0) REVERT: A 375 HIS cc_start: 0.8406 (m-70) cc_final: 0.8160 (m90) REVERT: A 462 PHE cc_start: 0.7824 (t80) cc_final: 0.7476 (t80) REVERT: A 480 GLU cc_start: 0.8915 (tt0) cc_final: 0.8604 (tp30) REVERT: A 484 GLU cc_start: 0.8002 (tp30) cc_final: 0.7316 (tp30) REVERT: A 487 ASN cc_start: 0.8443 (m-40) cc_final: 0.7598 (t0) REVERT: A 497 TYR cc_start: 0.7747 (p90) cc_final: 0.7468 (p90) REVERT: A 523 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8466 (mtm) REVERT: A 583 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: A 880 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.3813 (tptt) outliers start: 42 outliers final: 19 residues processed: 132 average time/residue: 0.9356 time to fit residues: 132.4052 Evaluate side-chains 128 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.163551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118613 restraints weight = 8356.069| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.01 r_work: 0.3343 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6789 Z= 0.293 Angle : 0.641 11.280 9186 Z= 0.307 Chirality : 0.043 0.175 1099 Planarity : 0.004 0.055 1174 Dihedral : 4.019 22.728 929 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.31 % Allowed : 34.50 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.28), residues: 878 helix: 1.47 (0.23), residues: 489 sheet: -0.99 (0.69), residues: 63 loop : -1.34 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 703 HIS 0.001 0.000 HIS A 552 PHE 0.009 0.001 PHE A 674 TYR 0.014 0.002 TYR A 831 ARG 0.011 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: A 29 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8623 (tptt) REVERT: A 153 GLU cc_start: 0.8113 (tt0) cc_final: 0.7336 (tm-30) REVERT: A 167 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: A 189 ASN cc_start: 0.9118 (p0) cc_final: 0.8835 (p0) REVERT: A 196 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7710 (tt) REVERT: A 226 GLU cc_start: 0.7489 (tt0) cc_final: 0.6906 (tt0) REVERT: A 234 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7607 (ttm-80) REVERT: A 292 GLU cc_start: 0.8624 (mp0) cc_final: 0.8117 (mp0) REVERT: A 375 HIS cc_start: 0.8425 (m-70) cc_final: 0.8178 (m90) REVERT: A 462 PHE cc_start: 0.7842 (t80) cc_final: 0.7504 (t80) REVERT: A 480 GLU cc_start: 0.8924 (tt0) cc_final: 0.8610 (tp30) REVERT: A 484 GLU cc_start: 0.8008 (tp30) cc_final: 0.7332 (tp30) REVERT: A 487 ASN cc_start: 0.8428 (m-40) cc_final: 0.7578 (t0) REVERT: A 497 TYR cc_start: 0.7796 (p90) cc_final: 0.7556 (p90) REVERT: A 523 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8520 (mtm) REVERT: A 583 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: A 880 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.3824 (tptt) outliers start: 38 outliers final: 20 residues processed: 135 average time/residue: 0.8974 time to fit residues: 129.7026 Evaluate side-chains 132 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 0.0030 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.165227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121287 restraints weight = 8382.759| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.00 r_work: 0.3397 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6789 Z= 0.224 Angle : 0.642 11.461 9186 Z= 0.306 Chirality : 0.042 0.177 1099 Planarity : 0.004 0.059 1174 Dihedral : 3.967 22.477 929 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.56 % Rotamer: Outliers : 4.33 % Allowed : 35.75 % Favored : 59.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.28), residues: 878 helix: 1.62 (0.23), residues: 489 sheet: -0.66 (0.74), residues: 58 loop : -1.36 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 703 HIS 0.001 0.000 HIS A 552 PHE 0.008 0.001 PHE A 455 TYR 0.013 0.002 TYR A 831 ARG 0.012 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8630 (tptt) REVERT: A 153 GLU cc_start: 0.8038 (tt0) cc_final: 0.7352 (tm-30) REVERT: A 167 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: A 226 GLU cc_start: 0.7364 (tt0) cc_final: 0.6852 (tt0) REVERT: A 234 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7568 (ttm-80) REVERT: A 292 GLU cc_start: 0.8547 (mp0) cc_final: 0.8045 (mp0) REVERT: A 375 HIS cc_start: 0.8397 (m-70) cc_final: 0.8165 (m90) REVERT: A 462 PHE cc_start: 0.7812 (t80) cc_final: 0.7462 (t80) REVERT: A 470 MET cc_start: 0.2329 (ppp) cc_final: 0.0989 (ptt) REVERT: A 480 GLU cc_start: 0.8916 (tt0) cc_final: 0.8581 (tp30) REVERT: A 484 GLU cc_start: 0.7999 (tp30) cc_final: 0.7343 (tp30) REVERT: A 487 ASN cc_start: 0.8379 (m-40) cc_final: 0.7533 (t0) REVERT: A 497 TYR cc_start: 0.7778 (p90) cc_final: 0.7355 (p90) REVERT: A 523 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8491 (mtm) REVERT: A 583 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8002 (mm-30) REVERT: A 880 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.3788 (tptt) outliers start: 31 outliers final: 17 residues processed: 126 average time/residue: 0.9126 time to fit residues: 123.1485 Evaluate side-chains 122 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.164092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119789 restraints weight = 8446.029| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.01 r_work: 0.3394 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6789 Z= 0.257 Angle : 0.652 12.064 9186 Z= 0.313 Chirality : 0.043 0.184 1099 Planarity : 0.004 0.061 1174 Dihedral : 3.991 22.536 929 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.67 % Rotamer: Outliers : 4.05 % Allowed : 36.17 % Favored : 59.78 % 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: 0.53 (0.28), residues: 878 helix: 1.58 (0.23), residues: 489 sheet: -0.70 (0.73), residues: 58 loop : -1.35 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 703 HIS 0.001 0.000 HIS A 552 PHE 0.009 0.001 PHE A 685 TYR 0.014 0.001 TYR A 831 ARG 0.013 0.001 ARG A 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8632 (tptt) REVERT: A 153 GLU cc_start: 0.8087 (tt0) cc_final: 0.7376 (tm-30) REVERT: A 167 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: A 226 GLU cc_start: 0.7381 (tt0) cc_final: 0.6853 (tt0) REVERT: A 234 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7582 (ttm-80) REVERT: A 292 GLU cc_start: 0.8584 (mp0) cc_final: 0.8155 (mp0) REVERT: A 375 HIS cc_start: 0.8392 (m-70) cc_final: 0.8150 (m90) REVERT: A 433 MET cc_start: 0.4510 (OUTLIER) cc_final: 0.2941 (mmt) REVERT: A 462 PHE cc_start: 0.7822 (t80) cc_final: 0.7506 (t80) REVERT: A 470 MET cc_start: 0.2353 (ppp) cc_final: 0.1033 (ptt) REVERT: A 480 GLU cc_start: 0.8924 (tt0) cc_final: 0.8593 (tp30) REVERT: A 484 GLU cc_start: 0.8022 (tp30) cc_final: 0.7364 (tp30) REVERT: A 487 ASN cc_start: 0.8394 (m-40) cc_final: 0.7547 (t0) REVERT: A 497 TYR cc_start: 0.7775 (p90) cc_final: 0.7350 (p90) REVERT: A 523 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8474 (mtm) REVERT: A 583 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: A 880 LYS cc_start: 0.5658 (OUTLIER) cc_final: 0.3844 (tptt) outliers start: 29 outliers final: 20 residues processed: 119 average time/residue: 0.9292 time to fit residues: 118.5396 Evaluate side-chains 123 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.164640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120668 restraints weight = 8402.526| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.00 r_work: 0.3393 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6789 Z= 0.235 Angle : 0.645 12.285 9186 Z= 0.309 Chirality : 0.043 0.174 1099 Planarity : 0.004 0.058 1174 Dihedral : 3.978 22.420 929 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Rotamer: Outliers : 4.33 % Allowed : 36.03 % Favored : 59.64 % 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: 0.56 (0.29), residues: 878 helix: 1.62 (0.23), residues: 489 sheet: -0.77 (0.67), residues: 72 loop : -1.35 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 703 HIS 0.001 0.000 HIS A 552 PHE 0.008 0.001 PHE A 685 TYR 0.012 0.001 TYR A 831 ARG 0.013 0.001 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5694.93 seconds wall clock time: 101 minutes 21.60 seconds (6081.60 seconds total)