Starting phenix.real_space_refine on Thu Mar 13 10:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xft_38309/03_2025/8xft_38309.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xft_38309/03_2025/8xft_38309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xft_38309/03_2025/8xft_38309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xft_38309/03_2025/8xft_38309.map" model { file = "/net/cci-nas-00/data/ceres_data/8xft_38309/03_2025/8xft_38309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xft_38309/03_2025/8xft_38309.cif" } resolution = 3.24 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= -0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5621 2.51 5 N 1462 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8742 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5728 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 697} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1349 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain breaks: 2 Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "G" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 789 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 5.68, per 1000 atoms: 0.65 Number of scatterers: 8742 At special positions: 0 Unit cell: (83.538, 88.893, 167.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1601 8.00 N 1462 7.00 C 5621 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 447 " - pdb=" SG CYS E 520 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 52 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 78 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 110 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 124 " distance=2.03 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 30.0% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.686A pdb=" N LYS A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 4.267A pdb=" N CYS A 339 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 538 through 567 removed outlier: 4.457A pdb=" N SER A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N CYS A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 605 through 615 removed outlier: 4.619A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 649 removed outlier: 4.215A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 Proline residue: A 680 - end of helix Processing helix chain 'A' and resid 694 through 699 removed outlier: 4.494A pdb=" N THR A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 694 through 699' Processing helix chain 'A' and resid 703 through 732 Processing helix chain 'A' and resid 740 through 769 removed outlier: 4.222A pdb=" N SER A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.816A pdb=" N CYS A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 805 through 820 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 185 through 198 Processing helix chain 'C' and resid 219 through 242 removed outlier: 3.673A pdb=" N LEU C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 removed outlier: 3.987A pdb=" N THR E 515 " --> pdb=" O PRO E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 537 removed outlier: 3.555A pdb=" N ILE E 536 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE E 537 " --> pdb=" O TRP E 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 533 through 537' Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.987A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 62 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 230 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 253 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 303 removed outlier: 6.769A pdb=" N ILE A 370 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA6, first strand: chain 'C' and resid 94 through 97 removed outlier: 6.102A pdb=" N VAL C 154 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL C 183 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 156 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY C 122 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP C 157 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL C 124 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AA8, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.372A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.372A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 69 through 75 removed outlier: 5.672A pdb=" N LEU G 63 " --> pdb=" O CYS G 93 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ARG G 95 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 14.775A pdb=" N ARG G 65 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 101 through 104 Processing sheet with id=AB3, first strand: chain 'G' and resid 118 through 119 337 hydrogen bonds defined for protein. 957 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: 2.84 Time building geometry restraints manager: 2.49 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: 2805 1.34 - 1.46: 2105 1.46 - 1.58: 3948 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8934 Sorted by residual: bond pdb=" N ILE A 192 " pdb=" CA ILE A 192 " ideal model delta sigma weight residual 1.454 1.462 -0.007 7.70e-03 1.69e+04 8.70e-01 bond pdb=" CA CYS A 761 " pdb=" C CYS A 761 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.26e-02 6.30e+03 6.49e-01 bond pdb=" CB THR A 329 " pdb=" CG2 THR A 329 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.62e-01 bond pdb=" CA LEU A 792 " pdb=" C LEU A 792 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.26e-02 6.30e+03 4.38e-01 bond pdb=" CB ASP A 137 " pdb=" CG ASP A 137 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.75e-01 ... (remaining 8929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 11770 1.25 - 2.50: 245 2.50 - 3.75: 80 3.75 - 5.00: 11 5.00 - 6.25: 8 Bond angle restraints: 12114 Sorted by residual: angle pdb=" N SER A 65 " pdb=" CA SER A 65 " pdb=" C SER A 65 " ideal model delta sigma weight residual 110.97 114.37 -3.40 1.09e+00 8.42e-01 9.71e+00 angle pdb=" N ASN A 233 " pdb=" CA ASN A 233 " pdb=" C ASN A 233 " ideal model delta sigma weight residual 111.03 113.92 -2.89 1.11e+00 8.12e-01 6.79e+00 angle pdb=" N PHE A 696 " pdb=" CA PHE A 696 " pdb=" C PHE A 696 " ideal model delta sigma weight residual 109.81 115.52 -5.71 2.21e+00 2.05e-01 6.67e+00 angle pdb=" N HIS A 209 " pdb=" CA HIS A 209 " pdb=" C HIS A 209 " ideal model delta sigma weight residual 111.03 113.78 -2.75 1.11e+00 8.12e-01 6.14e+00 angle pdb=" C SER A 191 " pdb=" N ILE A 192 " pdb=" CA ILE A 192 " ideal model delta sigma weight residual 122.85 120.74 2.11 8.70e-01 1.32e+00 5.91e+00 ... (remaining 12109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.85: 4871 13.85 - 27.71: 361 27.71 - 41.56: 95 41.56 - 55.42: 13 55.42 - 69.27: 7 Dihedral angle restraints: 5347 sinusoidal: 2105 harmonic: 3242 Sorted by residual: dihedral pdb=" CB CYS A 471 " pdb=" SG CYS A 471 " pdb=" SG CYS A 532 " pdb=" CB CYS A 532 " ideal model delta sinusoidal sigma weight residual 93.00 162.08 -69.08 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS G 78 " pdb=" SG CYS G 78 " pdb=" SG CYS G 93 " pdb=" CB CYS G 93 " ideal model delta sinusoidal sigma weight residual 93.00 151.62 -58.62 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS G 113 " pdb=" SG CYS G 113 " pdb=" SG CYS G 124 " pdb=" CB CYS G 124 " ideal model delta sinusoidal sigma weight residual 93.00 135.51 -42.51 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 5344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 859 0.031 - 0.062: 348 0.062 - 0.093: 107 0.093 - 0.123: 67 0.123 - 0.154: 12 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA PHE A 696 " pdb=" N PHE A 696 " pdb=" C PHE A 696 " pdb=" CB PHE A 696 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA CYS A 761 " pdb=" N CYS A 761 " pdb=" C CYS A 761 " pdb=" CB CYS A 761 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE C 205 " pdb=" N ILE C 205 " pdb=" C ILE C 205 " pdb=" CB ILE C 205 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1390 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 790 " -0.022 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 791 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 791 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 791 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 679 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 680 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 680 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 680 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 97 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.63e+00 pdb=" N PRO A 98 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " 0.018 5.00e-02 4.00e+02 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 865 2.75 - 3.28: 8648 3.28 - 3.82: 14542 3.82 - 4.36: 17425 4.36 - 4.90: 30050 Nonbonded interactions: 71530 Sorted by model distance: nonbonded pdb=" O ASN A 67 " pdb=" ND2 ASN A 91 " model vdw 2.208 3.120 nonbonded pdb=" O ASN A 139 " pdb=" ND2 ASN A 163 " model vdw 2.223 3.120 nonbonded pdb=" OH TYR A 468 " pdb=" OE2 GLU A 613 " model vdw 2.283 3.040 nonbonded pdb=" NZ LYS E 500 " pdb=" OG1 THR E 502 " model vdw 2.292 3.120 nonbonded pdb=" OD1 ASN C 108 " pdb=" NH1 ARG C 145 " model vdw 2.311 3.120 ... (remaining 71525 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.950 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 0.024 8934 Z= 0.194 Angle : 0.524 6.250 12114 Z= 0.272 Chirality : 0.042 0.154 1393 Planarity : 0.003 0.032 1541 Dihedral : 10.574 66.703 3212 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.54 % Allowed : 6.90 % Favored : 91.56 % 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: 0.22 (0.27), residues: 1102 helix: 2.23 (0.30), residues: 309 sheet: -0.18 (0.40), residues: 197 loop : -0.87 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.006 0.001 HIS A 256 PHE 0.012 0.001 PHE A 754 TYR 0.012 0.001 TYR C 182 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.978 Fit side-chains REVERT: A 458 ASN cc_start: 0.8700 (m-40) cc_final: 0.8374 (m110) REVERT: A 460 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8328 (mtp85) REVERT: A 683 HIS cc_start: 0.6674 (t-90) cc_final: 0.6026 (t-90) REVERT: A 765 PHE cc_start: 0.8423 (t80) cc_final: 0.7974 (t80) REVERT: C 234 LEU cc_start: 0.8679 (tp) cc_final: 0.8150 (mm) REVERT: E 497 ASP cc_start: 0.7625 (m-30) cc_final: 0.6538 (t0) REVERT: E 514 ASP cc_start: 0.8232 (t0) cc_final: 0.7900 (t0) REVERT: G 68 MET cc_start: 0.7175 (mtm) cc_final: 0.6843 (mtp) REVERT: G 73 GLU cc_start: 0.7879 (pt0) cc_final: 0.7414 (pt0) REVERT: G 90 MET cc_start: 0.7783 (ptm) cc_final: 0.7567 (ptm) REVERT: G 92 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7562 (mtm-85) REVERT: G 99 GLU cc_start: 0.8302 (pp20) cc_final: 0.8023 (pp20) REVERT: G 100 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7871 (m-40) REVERT: G 112 LYS cc_start: 0.8245 (ttpp) cc_final: 0.8027 (tmmt) REVERT: G 140 GLU cc_start: 0.7123 (pm20) cc_final: 0.6892 (pm20) outliers start: 15 outliers final: 6 residues processed: 144 average time/residue: 0.2544 time to fit residues: 48.6713 Evaluate side-chains 109 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0040 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 320 HIS C 100 GLN C 161 ASN C 167 GLN E 496 GLN E 506 GLN G 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104218 restraints weight = 13206.464| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.47 r_work: 0.2989 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 8934 Z= 0.173 Angle : 0.542 7.454 12114 Z= 0.274 Chirality : 0.043 0.173 1393 Planarity : 0.003 0.032 1541 Dihedral : 5.182 53.314 1199 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.47 % Allowed : 8.86 % Favored : 88.67 % 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: 0.24 (0.27), residues: 1102 helix: 2.16 (0.30), residues: 303 sheet: -0.14 (0.39), residues: 203 loop : -0.80 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.006 0.001 HIS A 256 PHE 0.014 0.001 PHE A 679 TYR 0.012 0.001 TYR C 182 ARG 0.006 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8111 (mp0) REVERT: A 604 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7447 (mtp180) REVERT: A 683 HIS cc_start: 0.6973 (t-90) cc_final: 0.6386 (t-90) REVERT: A 765 PHE cc_start: 0.8342 (t80) cc_final: 0.7934 (t80) REVERT: C 167 GLN cc_start: 0.7465 (mm-40) cc_final: 0.6960 (mm-40) REVERT: C 234 LEU cc_start: 0.8762 (tp) cc_final: 0.8209 (mm) REVERT: E 453 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7713 (m) REVERT: E 497 ASP cc_start: 0.7374 (m-30) cc_final: 0.6642 (t0) REVERT: E 514 ASP cc_start: 0.8268 (t0) cc_final: 0.7917 (t0) REVERT: E 517 MET cc_start: 0.8900 (tpp) cc_final: 0.8659 (tpp) REVERT: G 68 MET cc_start: 0.6967 (mtm) cc_final: 0.6698 (mtp) REVERT: G 92 ARG cc_start: 0.8376 (mmm160) cc_final: 0.8173 (mtm-85) REVERT: G 140 GLU cc_start: 0.7914 (pm20) cc_final: 0.7641 (pm20) outliers start: 24 outliers final: 8 residues processed: 125 average time/residue: 0.2414 time to fit residues: 40.5139 Evaluate side-chains 105 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 161 ASN G 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102210 restraints weight = 13306.701| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.42 r_work: 0.2957 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8934 Z= 0.258 Angle : 0.558 6.247 12114 Z= 0.284 Chirality : 0.044 0.155 1393 Planarity : 0.003 0.033 1541 Dihedral : 5.181 53.998 1194 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.88 % Allowed : 9.58 % Favored : 87.54 % 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: 0.25 (0.27), residues: 1102 helix: 2.18 (0.30), residues: 295 sheet: -0.09 (0.40), residues: 201 loop : -0.78 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.008 0.001 HIS A 256 PHE 0.018 0.001 PHE A 766 TYR 0.012 0.001 TYR C 182 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8134 (mp0) REVERT: A 279 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9132 (pp) REVERT: A 683 HIS cc_start: 0.6941 (t-90) cc_final: 0.6380 (t-90) REVERT: A 765 PHE cc_start: 0.8357 (t80) cc_final: 0.7993 (t80) REVERT: C 234 LEU cc_start: 0.8669 (tp) cc_final: 0.8152 (mm) REVERT: E 497 ASP cc_start: 0.7589 (m-30) cc_final: 0.6744 (t0) REVERT: E 514 ASP cc_start: 0.8298 (t0) cc_final: 0.7956 (t0) REVERT: E 517 MET cc_start: 0.8858 (tpp) cc_final: 0.8600 (tpp) REVERT: G 68 MET cc_start: 0.7040 (mtm) cc_final: 0.6796 (mtp) REVERT: G 99 GLU cc_start: 0.8410 (pp20) cc_final: 0.8064 (pp20) REVERT: G 112 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8752 (ttpp) REVERT: G 135 LEU cc_start: 0.7754 (tp) cc_final: 0.7480 (tt) REVERT: G 140 GLU cc_start: 0.7846 (pm20) cc_final: 0.7583 (pm20) outliers start: 28 outliers final: 14 residues processed: 125 average time/residue: 0.2460 time to fit residues: 41.7647 Evaluate side-chains 110 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 101 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103060 restraints weight = 13299.832| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.47 r_work: 0.2966 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8934 Z= 0.225 Angle : 0.553 6.543 12114 Z= 0.281 Chirality : 0.044 0.173 1393 Planarity : 0.003 0.039 1541 Dihedral : 5.169 55.003 1194 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.09 % Allowed : 10.61 % Favored : 86.30 % 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: 0.25 (0.27), residues: 1102 helix: 2.18 (0.30), residues: 294 sheet: -0.10 (0.40), residues: 201 loop : -0.77 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.007 0.001 HIS A 209 PHE 0.012 0.001 PHE A 808 TYR 0.012 0.001 TYR C 182 ARG 0.008 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8183 (mp0) REVERT: A 279 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9081 (pp) REVERT: A 598 ASP cc_start: 0.9331 (OUTLIER) cc_final: 0.8762 (t0) REVERT: A 683 HIS cc_start: 0.6968 (t-90) cc_final: 0.6394 (t-90) REVERT: C 234 LEU cc_start: 0.8685 (tp) cc_final: 0.8162 (mm) REVERT: E 497 ASP cc_start: 0.7534 (m-30) cc_final: 0.6753 (t0) REVERT: E 514 ASP cc_start: 0.8188 (t0) cc_final: 0.7883 (t0) REVERT: E 517 MET cc_start: 0.8863 (tpp) cc_final: 0.8662 (tpp) REVERT: G 68 MET cc_start: 0.6907 (mtm) cc_final: 0.6668 (mtp) REVERT: G 99 GLU cc_start: 0.8412 (pp20) cc_final: 0.8179 (pp20) REVERT: G 112 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8793 (ttpp) REVERT: G 140 GLU cc_start: 0.7820 (pm20) cc_final: 0.7569 (pm20) outliers start: 30 outliers final: 20 residues processed: 126 average time/residue: 0.2176 time to fit residues: 37.6167 Evaluate side-chains 120 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 138 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 44 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: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103176 restraints weight = 13196.561| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.41 r_work: 0.2956 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8934 Z= 0.234 Angle : 0.554 6.361 12114 Z= 0.281 Chirality : 0.044 0.202 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.193 55.493 1194 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.30 % Allowed : 11.23 % Favored : 85.48 % 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: 0.27 (0.27), residues: 1102 helix: 2.24 (0.30), residues: 294 sheet: -0.07 (0.40), residues: 201 loop : -0.79 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.007 0.001 HIS A 209 PHE 0.012 0.001 PHE A 808 TYR 0.012 0.001 TYR C 182 ARG 0.004 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9095 (pp) REVERT: A 598 ASP cc_start: 0.9334 (OUTLIER) cc_final: 0.8769 (t0) REVERT: A 683 HIS cc_start: 0.7057 (t-90) cc_final: 0.6493 (t-90) REVERT: C 234 LEU cc_start: 0.8691 (tp) cc_final: 0.8163 (mm) REVERT: E 497 ASP cc_start: 0.7549 (m-30) cc_final: 0.6766 (t0) REVERT: E 514 ASP cc_start: 0.8225 (t0) cc_final: 0.7966 (t0) REVERT: E 517 MET cc_start: 0.8859 (tpp) cc_final: 0.8657 (tpp) REVERT: G 68 MET cc_start: 0.6896 (mtm) cc_final: 0.6639 (mtp) REVERT: G 112 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8801 (ttpp) REVERT: G 135 LEU cc_start: 0.7712 (tp) cc_final: 0.7414 (tt) REVERT: G 140 GLU cc_start: 0.7798 (pm20) cc_final: 0.7553 (pm20) outliers start: 32 outliers final: 20 residues processed: 126 average time/residue: 0.2242 time to fit residues: 38.4916 Evaluate side-chains 118 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 756 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105657 restraints weight = 13132.125| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.42 r_work: 0.3043 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 8934 Z= 0.247 Angle : 0.567 6.406 12114 Z= 0.290 Chirality : 0.045 0.201 1393 Planarity : 0.003 0.035 1541 Dihedral : 5.243 56.804 1194 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.30 % Allowed : 11.43 % Favored : 85.27 % 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: 0.26 (0.27), residues: 1102 helix: 2.25 (0.30), residues: 294 sheet: -0.10 (0.40), residues: 201 loop : -0.79 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.008 0.001 HIS A 209 PHE 0.024 0.001 PHE A 754 TYR 0.012 0.001 TYR C 182 ARG 0.003 0.000 ARG C 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 279 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9114 (pp) REVERT: A 598 ASP cc_start: 0.9332 (OUTLIER) cc_final: 0.8771 (t0) REVERT: A 683 HIS cc_start: 0.7036 (t-90) cc_final: 0.6441 (t-90) REVERT: C 193 ASN cc_start: 0.8720 (m110) cc_final: 0.8486 (m110) REVERT: C 234 LEU cc_start: 0.8696 (tp) cc_final: 0.8161 (mm) REVERT: E 497 ASP cc_start: 0.7633 (m-30) cc_final: 0.6854 (t0) REVERT: E 514 ASP cc_start: 0.8233 (t0) cc_final: 0.8003 (t0) REVERT: E 517 MET cc_start: 0.8823 (tpp) cc_final: 0.8613 (tpp) REVERT: G 68 MET cc_start: 0.6926 (mtm) cc_final: 0.6656 (mtp) REVERT: G 99 GLU cc_start: 0.8391 (pp20) cc_final: 0.8161 (pp20) REVERT: G 112 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8774 (ttpp) REVERT: G 140 GLU cc_start: 0.7764 (pm20) cc_final: 0.7526 (pm20) outliers start: 32 outliers final: 21 residues processed: 126 average time/residue: 0.2389 time to fit residues: 41.7052 Evaluate side-chains 120 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 39 optimal weight: 0.0870 chunk 35 optimal weight: 0.0870 chunk 76 optimal weight: 0.0870 chunk 106 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104825 restraints weight = 13235.206| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.43 r_work: 0.3002 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 8934 Z= 0.148 Angle : 0.539 6.828 12114 Z= 0.269 Chirality : 0.043 0.205 1393 Planarity : 0.003 0.035 1541 Dihedral : 4.993 57.862 1194 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.88 % Allowed : 12.98 % Favored : 84.14 % 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: 0.36 (0.27), residues: 1102 helix: 2.40 (0.30), residues: 290 sheet: -0.13 (0.40), residues: 203 loop : -0.71 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.006 0.001 HIS A 209 PHE 0.011 0.001 PHE A 706 TYR 0.014 0.001 TYR E 504 ARG 0.003 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 598 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.8777 (t0) REVERT: A 683 HIS cc_start: 0.6928 (t-90) cc_final: 0.6400 (t-90) REVERT: C 120 TRP cc_start: 0.7268 (p-90) cc_final: 0.6696 (p-90) REVERT: C 234 LEU cc_start: 0.8652 (tp) cc_final: 0.8120 (mm) REVERT: E 497 ASP cc_start: 0.7538 (m-30) cc_final: 0.6737 (t0) REVERT: E 514 ASP cc_start: 0.8209 (t0) cc_final: 0.7915 (t0) REVERT: G 68 MET cc_start: 0.6999 (mtm) cc_final: 0.6701 (mtp) REVERT: G 99 GLU cc_start: 0.8315 (pp20) cc_final: 0.8026 (pp20) REVERT: G 112 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8714 (ttpp) REVERT: G 135 LEU cc_start: 0.7722 (tp) cc_final: 0.7409 (tt) REVERT: G 140 GLU cc_start: 0.7694 (pm20) cc_final: 0.7415 (pm20) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.2180 time to fit residues: 37.8567 Evaluate side-chains 121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 110 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102019 restraints weight = 13399.332| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.48 r_work: 0.2955 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8934 Z= 0.257 Angle : 0.575 6.721 12114 Z= 0.292 Chirality : 0.045 0.202 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.213 57.855 1194 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.37 % Allowed : 13.08 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.27), residues: 1102 helix: 2.21 (0.30), residues: 295 sheet: -0.22 (0.39), residues: 211 loop : -0.72 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.007 0.001 HIS A 209 PHE 0.028 0.001 PHE A 808 TYR 0.011 0.001 TYR E 504 ARG 0.003 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 598 ASP cc_start: 0.9341 (OUTLIER) cc_final: 0.8773 (t0) REVERT: A 683 HIS cc_start: 0.6875 (t-90) cc_final: 0.6342 (t-90) REVERT: C 234 LEU cc_start: 0.8589 (tp) cc_final: 0.8072 (mm) REVERT: E 497 ASP cc_start: 0.7685 (m-30) cc_final: 0.6829 (t0) REVERT: E 514 ASP cc_start: 0.8258 (t0) cc_final: 0.8005 (t0) REVERT: G 68 MET cc_start: 0.6953 (mtm) cc_final: 0.6668 (mtp) REVERT: G 99 GLU cc_start: 0.8344 (pp20) cc_final: 0.8045 (pp20) REVERT: G 112 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8741 (ttpp) REVERT: G 135 LEU cc_start: 0.7705 (tp) cc_final: 0.7403 (tt) REVERT: G 140 GLU cc_start: 0.7735 (pm20) cc_final: 0.7502 (pm20) outliers start: 23 outliers final: 18 residues processed: 116 average time/residue: 0.2397 time to fit residues: 38.4252 Evaluate side-chains 117 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102375 restraints weight = 13275.950| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.41 r_work: 0.2969 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8934 Z= 0.232 Angle : 0.575 7.419 12114 Z= 0.291 Chirality : 0.044 0.210 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.216 59.271 1194 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.57 % Allowed : 12.98 % Favored : 84.45 % 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: 0.23 (0.27), residues: 1102 helix: 2.19 (0.30), residues: 295 sheet: -0.24 (0.39), residues: 209 loop : -0.75 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.007 0.001 HIS A 209 PHE 0.026 0.001 PHE A 808 TYR 0.012 0.001 TYR E 504 ARG 0.005 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.902 Fit side-chains REVERT: A 598 ASP cc_start: 0.9333 (OUTLIER) cc_final: 0.8766 (t0) REVERT: A 683 HIS cc_start: 0.6909 (t-90) cc_final: 0.6384 (t-90) REVERT: C 120 TRP cc_start: 0.7256 (p-90) cc_final: 0.6760 (p-90) REVERT: C 234 LEU cc_start: 0.8691 (tp) cc_final: 0.8157 (mm) REVERT: E 497 ASP cc_start: 0.7664 (m-30) cc_final: 0.6804 (t0) REVERT: E 504 TYR cc_start: 0.8223 (m-80) cc_final: 0.7984 (m-80) REVERT: E 514 ASP cc_start: 0.8248 (t0) cc_final: 0.7993 (t0) REVERT: G 68 MET cc_start: 0.7045 (mtm) cc_final: 0.6752 (mtp) REVERT: G 92 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8275 (mmm160) REVERT: G 99 GLU cc_start: 0.8338 (pp20) cc_final: 0.8057 (pp20) REVERT: G 112 LYS cc_start: 0.9030 (ttpp) cc_final: 0.8748 (ttpp) REVERT: G 135 LEU cc_start: 0.7695 (tp) cc_final: 0.7406 (tt) REVERT: G 140 GLU cc_start: 0.7725 (pm20) cc_final: 0.7494 (pm20) outliers start: 25 outliers final: 21 residues processed: 119 average time/residue: 0.2335 time to fit residues: 38.1847 Evaluate side-chains 120 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102748 restraints weight = 13200.372| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.36 r_work: 0.2973 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8934 Z= 0.217 Angle : 0.589 9.403 12114 Z= 0.298 Chirality : 0.045 0.373 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.252 59.658 1194 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.47 % Allowed : 13.18 % Favored : 84.35 % 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: 0.24 (0.27), residues: 1102 helix: 2.20 (0.30), residues: 295 sheet: -0.23 (0.39), residues: 211 loop : -0.75 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.007 0.001 HIS A 209 PHE 0.025 0.001 PHE A 808 TYR 0.011 0.001 TYR E 504 ARG 0.005 0.000 ARG G 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.966 Fit side-chains REVERT: A 598 ASP cc_start: 0.9331 (OUTLIER) cc_final: 0.8766 (t0) REVERT: A 683 HIS cc_start: 0.6880 (t-90) cc_final: 0.6359 (t-90) REVERT: C 120 TRP cc_start: 0.7246 (p-90) cc_final: 0.6750 (p-90) REVERT: C 234 LEU cc_start: 0.8692 (tp) cc_final: 0.8158 (mm) REVERT: E 497 ASP cc_start: 0.7659 (m-30) cc_final: 0.6798 (t0) REVERT: E 504 TYR cc_start: 0.8225 (m-80) cc_final: 0.7993 (m-80) REVERT: E 514 ASP cc_start: 0.8300 (t0) cc_final: 0.8061 (t0) REVERT: G 68 MET cc_start: 0.7172 (mtm) cc_final: 0.6873 (mtp) REVERT: G 99 GLU cc_start: 0.8333 (pp20) cc_final: 0.8079 (pp20) REVERT: G 112 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8730 (ttpp) REVERT: G 135 LEU cc_start: 0.7697 (tp) cc_final: 0.7385 (tt) REVERT: G 140 GLU cc_start: 0.7746 (pm20) cc_final: 0.7519 (pm20) outliers start: 24 outliers final: 20 residues processed: 113 average time/residue: 0.2343 time to fit residues: 36.8349 Evaluate side-chains 116 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106696 restraints weight = 13364.125| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.61 r_work: 0.3038 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8934 Z= 0.251 Angle : 0.640 23.201 12114 Z= 0.324 Chirality : 0.046 0.305 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.368 59.037 1194 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.27 % Allowed : 13.29 % Favored : 84.45 % 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: 0.22 (0.27), residues: 1102 helix: 2.17 (0.30), residues: 295 sheet: -0.23 (0.39), residues: 211 loop : -0.75 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.008 0.001 HIS A 209 PHE 0.026 0.001 PHE A 808 TYR 0.012 0.001 TYR E 504 ARG 0.003 0.000 ARG C 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5354.43 seconds wall clock time: 93 minutes 2.13 seconds (5582.13 seconds total)