Starting phenix.real_space_refine on Sat Dec 28 16:36:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xft_38309/12_2024/8xft_38309.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xft_38309/12_2024/8xft_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_38309/12_2024/8xft_38309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xft_38309/12_2024/8xft_38309.map" model { file = "/net/cci-nas-00/data/ceres_data/8xft_38309/12_2024/8xft_38309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xft_38309/12_2024/8xft_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.97, per 1000 atoms: 0.68 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: 2.37 Conformation dependent library (CDL) restraints added in 1.0 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: 1.18 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: 2.73 Time building geometry restraints manager: 2.69 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: 2.540 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.170 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- 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 : 0.942 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: 0.2584 time to fit residues: 49.4144 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 : 1.046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 1.059 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8015 (mp0) REVERT: A 231 ASP cc_start: 0.8731 (t0) cc_final: 0.8299 (t0) REVERT: A 275 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8402 (mtt-85) REVERT: A 458 ASN cc_start: 0.8715 (m-40) cc_final: 0.8399 (m110) REVERT: A 604 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.6961 (mtp180) REVERT: A 683 HIS cc_start: 0.6637 (t-90) cc_final: 0.5963 (t-90) REVERT: A 765 PHE cc_start: 0.8425 (t80) cc_final: 0.7957 (t80) REVERT: C 167 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6885 (mm-40) REVERT: C 234 LEU cc_start: 0.8651 (tp) cc_final: 0.8109 (mm) REVERT: E 453 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8093 (m) REVERT: E 497 ASP cc_start: 0.7703 (m-30) cc_final: 0.6557 (t0) REVERT: E 514 ASP cc_start: 0.8348 (t0) cc_final: 0.7944 (t0) REVERT: E 517 MET cc_start: 0.8749 (tpp) cc_final: 0.8341 (tpp) REVERT: G 68 MET cc_start: 0.7158 (mtm) cc_final: 0.6791 (mtp) REVERT: G 90 MET cc_start: 0.7769 (ptm) cc_final: 0.7556 (ptm) REVERT: G 92 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7529 (mtm-85) REVERT: G 99 GLU cc_start: 0.8299 (pp20) cc_final: 0.7965 (pp20) REVERT: G 140 GLU cc_start: 0.7274 (pm20) cc_final: 0.6997 (pm20) outliers start: 24 outliers final: 8 residues processed: 125 average time/residue: 0.2495 time to fit residues: 41.9557 Evaluate side-chains 107 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8934 Z= 0.199 Angle : 0.533 6.475 12114 Z= 0.270 Chirality : 0.043 0.152 1393 Planarity : 0.003 0.032 1541 Dihedral : 5.038 53.765 1194 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.57 % Allowed : 9.37 % Favored : 88.05 % 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: 0.32 (0.27), residues: 1102 helix: 2.23 (0.30), residues: 295 sheet: -0.07 (0.40), residues: 203 loop : -0.72 (0.26), residues: 604 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 0.018 0.001 PHE A 766 TYR 0.012 0.001 TYR C 182 ARG 0.003 0.000 ARG G 64 *********************** 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 129 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8015 (mp0) REVERT: A 231 ASP cc_start: 0.8756 (t0) cc_final: 0.8332 (t0) REVERT: A 458 ASN cc_start: 0.8754 (m-40) cc_final: 0.8433 (m110) REVERT: A 604 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7071 (mtp180) REVERT: A 683 HIS cc_start: 0.6670 (t-90) cc_final: 0.5991 (t-90) REVERT: A 765 PHE cc_start: 0.8413 (t80) cc_final: 0.8010 (t80) REVERT: C 234 LEU cc_start: 0.8638 (tp) cc_final: 0.8103 (mm) REVERT: E 497 ASP cc_start: 0.7875 (m-30) cc_final: 0.6637 (t0) REVERT: E 514 ASP cc_start: 0.8353 (t0) cc_final: 0.7966 (t0) REVERT: E 517 MET cc_start: 0.8716 (tpp) cc_final: 0.8315 (tpp) REVERT: G 68 MET cc_start: 0.7143 (mtm) cc_final: 0.6771 (mtp) REVERT: G 90 MET cc_start: 0.7788 (ptm) cc_final: 0.7497 (ptm) REVERT: G 92 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7549 (mtm-85) REVERT: G 99 GLU cc_start: 0.8312 (pp20) cc_final: 0.8020 (pp20) REVERT: G 112 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8160 (ttpp) REVERT: G 135 LEU cc_start: 0.7637 (tp) cc_final: 0.7386 (tt) REVERT: G 140 GLU cc_start: 0.7220 (pm20) cc_final: 0.6972 (pm20) outliers start: 25 outliers final: 12 residues processed: 121 average time/residue: 0.2553 time to fit residues: 41.9340 Evaluate side-chains 110 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 344 MET 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 98 ILE Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 8934 Z= 0.241 Angle : 0.555 6.989 12114 Z= 0.282 Chirality : 0.044 0.164 1393 Planarity : 0.003 0.040 1541 Dihedral : 5.182 54.875 1194 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.88 % Allowed : 9.99 % Favored : 87.13 % 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: 2.18 (0.30), residues: 294 sheet: -0.06 (0.40), residues: 201 loop : -0.76 (0.26), residues: 607 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 0.012 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 132 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8056 (mp0) REVERT: A 231 ASP cc_start: 0.8747 (t0) cc_final: 0.8355 (t0) REVERT: A 279 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9152 (pp) REVERT: A 458 ASN cc_start: 0.8777 (m-40) cc_final: 0.8432 (m110) REVERT: A 598 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8643 (t0) REVERT: A 683 HIS cc_start: 0.6722 (t-90) cc_final: 0.6044 (t-90) REVERT: A 788 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8426 (mp) REVERT: C 234 LEU cc_start: 0.8560 (tp) cc_final: 0.8046 (mm) REVERT: E 497 ASP cc_start: 0.7886 (m-30) cc_final: 0.6663 (t0) REVERT: E 514 ASP cc_start: 0.8331 (t0) cc_final: 0.7916 (t0) REVERT: E 517 MET cc_start: 0.8701 (tpp) cc_final: 0.8260 (tpp) REVERT: G 68 MET cc_start: 0.7207 (mtm) cc_final: 0.6878 (mtp) REVERT: G 90 MET cc_start: 0.7874 (ptm) cc_final: 0.7545 (ptm) REVERT: G 92 ARG cc_start: 0.8095 (mmm160) cc_final: 0.7565 (mtm-85) REVERT: G 99 GLU cc_start: 0.8283 (pp20) cc_final: 0.8023 (pp20) REVERT: G 102 ASP cc_start: 0.8778 (t0) cc_final: 0.8178 (t0) REVERT: G 140 GLU cc_start: 0.7178 (pm20) cc_final: 0.6950 (pm20) outliers start: 28 outliers final: 19 residues processed: 126 average time/residue: 0.2181 time to fit residues: 37.8708 Evaluate side-chains 121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 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 783 LYS Chi-restraints excluded: chain A residue 788 ILE 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 107 LYS 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 1 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 0.0000 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8934 Z= 0.222 Angle : 0.546 6.411 12114 Z= 0.277 Chirality : 0.043 0.162 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.159 55.364 1194 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.99 % Allowed : 11.12 % Favored : 85.89 % 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: 0.25 (0.27), residues: 1102 helix: 2.16 (0.30), residues: 294 sheet: -0.09 (0.40), residues: 201 loop : -0.76 (0.26), residues: 607 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 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 129 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8064 (mp0) REVERT: A 231 ASP cc_start: 0.8741 (t0) cc_final: 0.8328 (t0) REVERT: A 279 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9150 (pp) REVERT: A 458 ASN cc_start: 0.8768 (m-40) cc_final: 0.8433 (m110) REVERT: A 598 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8623 (t0) REVERT: A 683 HIS cc_start: 0.6669 (t-90) cc_final: 0.5982 (t-90) REVERT: C 234 LEU cc_start: 0.8562 (tp) cc_final: 0.8046 (mm) REVERT: E 497 ASP cc_start: 0.7892 (m-30) cc_final: 0.6667 (t0) REVERT: E 514 ASP cc_start: 0.8352 (t0) cc_final: 0.8040 (t0) REVERT: E 517 MET cc_start: 0.8720 (tpp) cc_final: 0.8285 (tpp) REVERT: G 68 MET cc_start: 0.7090 (mtm) cc_final: 0.6706 (mtp) REVERT: G 99 GLU cc_start: 0.8301 (pp20) cc_final: 0.8024 (pp20) REVERT: G 135 LEU cc_start: 0.7620 (tp) cc_final: 0.7341 (tt) REVERT: G 140 GLU cc_start: 0.7126 (pm20) cc_final: 0.6892 (pm20) outliers start: 29 outliers final: 20 residues processed: 122 average time/residue: 0.2318 time to fit residues: 38.8934 Evaluate side-chains 119 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 Chi-restraints excluded: chain G residue 138 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 8934 Z= 0.225 Angle : 0.550 6.497 12114 Z= 0.279 Chirality : 0.044 0.210 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.160 55.700 1194 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.99 % Allowed : 11.53 % 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: 0.25 (0.27), residues: 1102 helix: 2.18 (0.30), residues: 294 sheet: -0.09 (0.40), residues: 201 loop : -0.76 (0.26), residues: 607 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 0.025 0.001 PHE A 754 TYR 0.012 0.001 TYR C 182 ARG 0.003 0.000 ARG A 135 *********************** 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 131 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.058 Fit side-chains REVERT: A 146 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8037 (mp0) REVERT: A 231 ASP cc_start: 0.8691 (t0) cc_final: 0.8263 (t0) REVERT: A 279 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9149 (pp) REVERT: A 458 ASN cc_start: 0.8770 (m-40) cc_final: 0.8436 (m110) REVERT: A 598 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8658 (t0) REVERT: A 683 HIS cc_start: 0.6578 (t-90) cc_final: 0.5914 (t-90) REVERT: C 120 TRP cc_start: 0.6679 (p-90) cc_final: 0.6238 (p-90) REVERT: C 173 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: C 234 LEU cc_start: 0.8564 (tp) cc_final: 0.8047 (mm) REVERT: E 497 ASP cc_start: 0.7928 (m-30) cc_final: 0.6735 (t0) REVERT: E 514 ASP cc_start: 0.8352 (t0) cc_final: 0.7987 (t0) REVERT: E 517 MET cc_start: 0.8696 (tpp) cc_final: 0.8255 (tpp) REVERT: G 68 MET cc_start: 0.7084 (mtm) cc_final: 0.6684 (mtp) REVERT: G 99 GLU cc_start: 0.8291 (pp20) cc_final: 0.7936 (pp20) REVERT: G 140 GLU cc_start: 0.7148 (pm20) cc_final: 0.6915 (pm20) outliers start: 29 outliers final: 19 residues processed: 124 average time/residue: 0.2350 time to fit residues: 40.2501 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 : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 Chi-restraints excluded: chain G residue 138 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.0370 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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** C 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 8934 Z= 0.185 Angle : 0.543 6.575 12114 Z= 0.273 Chirality : 0.043 0.200 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.093 56.945 1194 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.78 % Allowed : 12.67 % 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: 0.27 (0.27), residues: 1102 helix: 2.18 (0.30), residues: 295 sheet: -0.12 (0.40), residues: 203 loop : -0.73 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.005 0.001 HIS A 256 PHE 0.018 0.001 PHE A 754 TYR 0.011 0.001 TYR C 182 ARG 0.003 0.000 ARG C 145 *********************** 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 136 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8029 (mp0) REVERT: A 231 ASP cc_start: 0.8687 (t0) cc_final: 0.8253 (t0) REVERT: A 279 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9131 (pp) REVERT: A 458 ASN cc_start: 0.8773 (m-40) cc_final: 0.8438 (m110) REVERT: A 598 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8657 (t0) REVERT: A 683 HIS cc_start: 0.6590 (t-90) cc_final: 0.5957 (t-90) REVERT: C 120 TRP cc_start: 0.6726 (p-90) cc_final: 0.6354 (p-90) REVERT: C 167 GLN cc_start: 0.7245 (mm110) cc_final: 0.6951 (mm-40) REVERT: C 173 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: C 187 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6852 (p0) REVERT: C 234 LEU cc_start: 0.8530 (tp) cc_final: 0.8005 (mm) REVERT: E 497 ASP cc_start: 0.7914 (m-30) cc_final: 0.6733 (t0) REVERT: E 514 ASP cc_start: 0.8332 (t0) cc_final: 0.7991 (t0) REVERT: E 517 MET cc_start: 0.8707 (tpp) cc_final: 0.8276 (tpp) REVERT: G 68 MET cc_start: 0.7208 (mtm) cc_final: 0.6798 (mtp) REVERT: G 99 GLU cc_start: 0.8291 (pp20) cc_final: 0.7959 (pp20) REVERT: G 102 ASP cc_start: 0.8708 (t0) cc_final: 0.8228 (t0) REVERT: G 140 GLU cc_start: 0.7047 (pm20) cc_final: 0.6833 (pm20) outliers start: 27 outliers final: 18 residues processed: 129 average time/residue: 0.2397 time to fit residues: 42.0673 Evaluate side-chains 125 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 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 187 ASP 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 Chi-restraints excluded: chain G residue 138 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.0010 chunk 102 optimal weight: 0.0980 chunk 93 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 overall best weight: 0.2944 ------------------------------------------------------------------------------- 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** A 756 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.002 0.059 8934 Z= 0.153 Angle : 0.558 12.781 12114 Z= 0.277 Chirality : 0.043 0.203 1393 Planarity : 0.003 0.044 1541 Dihedral : 4.935 57.357 1194 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.57 % Allowed : 12.77 % Favored : 84.65 % 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: 0.39 (0.27), residues: 1102 helix: 2.28 (0.31), residues: 290 sheet: -0.08 (0.40), residues: 205 loop : -0.62 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 PHE 0.024 0.001 PHE A 808 TYR 0.010 0.001 TYR C 182 ARG 0.012 0.000 ARG A 275 *********************** 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 132 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7930 (mp0) REVERT: A 231 ASP cc_start: 0.8678 (t0) cc_final: 0.8206 (t0) REVERT: A 275 ARG cc_start: 0.8794 (mtm110) cc_final: 0.8398 (mtm180) REVERT: A 458 ASN cc_start: 0.8754 (m-40) cc_final: 0.8423 (m110) REVERT: A 598 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8649 (t0) REVERT: A 683 HIS cc_start: 0.6440 (t-90) cc_final: 0.5866 (t-90) REVERT: A 768 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7693 (t80) REVERT: C 120 TRP cc_start: 0.6696 (p-90) cc_final: 0.6260 (p-90) REVERT: C 173 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: C 187 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6856 (p0) REVERT: C 234 LEU cc_start: 0.8564 (tp) cc_final: 0.8094 (mm) REVERT: E 497 ASP cc_start: 0.7889 (m-30) cc_final: 0.6704 (t0) REVERT: E 514 ASP cc_start: 0.8374 (t0) cc_final: 0.8049 (t0) REVERT: E 517 MET cc_start: 0.8727 (tpp) cc_final: 0.8325 (tpp) REVERT: G 99 GLU cc_start: 0.8298 (pp20) cc_final: 0.7951 (pp20) REVERT: G 102 ASP cc_start: 0.8708 (t0) cc_final: 0.8217 (t0) REVERT: G 140 GLU cc_start: 0.6921 (pm20) cc_final: 0.6715 (pm20) outliers start: 25 outliers final: 15 residues processed: 125 average time/residue: 0.2395 time to fit residues: 40.7854 Evaluate side-chains 122 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 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 768 PHE 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 187 ASP 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 Chi-restraints excluded: chain G residue 138 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN C 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8934 Z= 0.258 Angle : 0.593 11.301 12114 Z= 0.298 Chirality : 0.044 0.195 1393 Planarity : 0.004 0.055 1541 Dihedral : 5.256 56.490 1194 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.27 % Allowed : 13.18 % 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: 0.27 (0.27), residues: 1102 helix: 2.08 (0.30), residues: 295 sheet: -0.08 (0.40), residues: 205 loop : -0.69 (0.27), residues: 602 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 0.026 0.001 PHE A 808 TYR 0.013 0.001 TYR E 504 ARG 0.010 0.000 ARG A 275 *********************** 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 123 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8041 (mp0) REVERT: A 231 ASP cc_start: 0.8694 (t0) cc_final: 0.8315 (t0) REVERT: A 458 ASN cc_start: 0.8827 (m-40) cc_final: 0.8460 (m110) REVERT: A 598 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8603 (t0) REVERT: A 683 HIS cc_start: 0.6471 (t-90) cc_final: 0.5896 (t-90) REVERT: A 768 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7725 (t80) REVERT: C 173 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: C 234 LEU cc_start: 0.8436 (tp) cc_final: 0.7922 (mm) REVERT: E 497 ASP cc_start: 0.7915 (m-30) cc_final: 0.6727 (t0) REVERT: E 514 ASP cc_start: 0.8327 (t0) cc_final: 0.8011 (t0) REVERT: E 517 MET cc_start: 0.8692 (tpp) cc_final: 0.8226 (tpp) REVERT: G 68 MET cc_start: 0.7208 (mtp) cc_final: 0.6587 (mtp) REVERT: G 99 GLU cc_start: 0.8312 (pp20) cc_final: 0.7956 (pp20) outliers start: 22 outliers final: 17 residues processed: 115 average time/residue: 0.2666 time to fit residues: 42.1124 Evaluate side-chains 119 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 768 PHE 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 E residue 511 LYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 138 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8934 Z= 0.281 Angle : 0.615 10.728 12114 Z= 0.310 Chirality : 0.045 0.204 1393 Planarity : 0.004 0.063 1541 Dihedral : 5.356 57.580 1194 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % 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: 0.20 (0.27), residues: 1102 helix: 1.99 (0.30), residues: 296 sheet: -0.12 (0.40), residues: 203 loop : -0.72 (0.26), residues: 603 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 0.026 0.001 PHE A 808 TYR 0.015 0.001 TYR E 504 ARG 0.014 0.000 ARG A 275 ********************** 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 123 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.956 Fit side-chains REVERT: A 146 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8063 (mp0) REVERT: A 231 ASP cc_start: 0.8736 (t0) cc_final: 0.8345 (t0) REVERT: A 458 ASN cc_start: 0.8798 (m-40) cc_final: 0.8442 (m110) REVERT: A 598 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8623 (t0) REVERT: A 683 HIS cc_start: 0.6542 (t-90) cc_final: 0.5919 (t-90) REVERT: A 768 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7772 (t80) REVERT: C 173 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: C 187 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6859 (p0) REVERT: C 234 LEU cc_start: 0.8572 (tp) cc_final: 0.8050 (mm) REVERT: E 497 ASP cc_start: 0.7859 (m-30) cc_final: 0.6718 (t0) REVERT: E 514 ASP cc_start: 0.8323 (t0) cc_final: 0.8044 (t0) REVERT: E 517 MET cc_start: 0.8691 (tpp) cc_final: 0.8156 (tpp) REVERT: G 99 GLU cc_start: 0.8318 (pp20) cc_final: 0.7957 (pp20) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.2425 time to fit residues: 38.3772 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 : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 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 698 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 768 PHE 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 187 ASP 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 107 LYS Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 138 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 90 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.0030 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.2186 ------------------------------------------------------------------------------- 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** G 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105251 restraints weight = 13075.037| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.34 r_work: 0.3023 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8934 Z= 0.154 Angle : 0.583 10.899 12114 Z= 0.292 Chirality : 0.044 0.336 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.072 59.284 1194 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.47 % Allowed : 13.39 % 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: 0.33 (0.27), residues: 1102 helix: 2.20 (0.31), residues: 290 sheet: -0.13 (0.40), residues: 205 loop : -0.64 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 159 HIS 0.004 0.001 HIS A 256 PHE 0.019 0.001 PHE A 808 TYR 0.011 0.001 TYR E 504 ARG 0.008 0.000 ARG A 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.00 seconds wall clock time: 38 minutes 36.86 seconds (2316.86 seconds total)