Starting phenix.real_space_refine on Wed Sep 17 13:06:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xft_38309/09_2025/8xft_38309.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xft_38309/09_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_38309/09_2025/8xft_38309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xft_38309/09_2025/8xft_38309.map" model { file = "/net/cci-nas-00/data/ceres_data/8xft_38309/09_2025/8xft_38309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xft_38309/09_2025/8xft_38309.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 2.21, per 1000 atoms: 0.25 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: 0.93 Conformation dependent library (CDL) restraints added in 366.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.34 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: 1.56 Time building geometry restraints manager: 1.19 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: 3.370 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.300 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- 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 8945 Z= 0.128 Angle : 0.525 6.250 12136 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 : 6.87 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (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 ARG 0.002 0.000 ARG A 135 TYR 0.012 0.001 TYR C 182 PHE 0.012 0.001 PHE A 754 TRP 0.011 0.001 TRP A 159 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8934) covalent geometry : angle 0.52353 (12114) SS BOND : bond 0.00182 ( 11) SS BOND : angle 0.93698 ( 22) hydrogen bonds : bond 0.07248 ( 326) hydrogen bonds : angle 4.07777 ( 957) *********************** 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 : 0.587 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: 0.7576 (ptm) REVERT: G 92 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7564 (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: 0.1237 time to fit residues: 23.5604 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 : 0.370 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 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 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 = 0.3754 r_free = 0.3754 target = 0.136558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103135 restraints weight = 13291.660| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.49 r_work: 0.2970 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 8945 Z= 0.141 Angle : 0.569 10.713 12136 Z= 0.287 Chirality : 0.044 0.198 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.285 53.292 1199 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.78 % Allowed : 8.44 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.26), residues: 1102 helix: 2.25 (0.30), residues: 297 sheet: -0.12 (0.39), residues: 203 loop : -0.81 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 275 TYR 0.012 0.001 TYR C 182 PHE 0.014 0.001 PHE A 679 TRP 0.011 0.001 TRP A 159 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8934) covalent geometry : angle 0.55833 (12114) SS BOND : bond 0.00841 ( 11) SS BOND : angle 2.60791 ( 22) hydrogen bonds : bond 0.03858 ( 326) hydrogen bonds : angle 3.96522 ( 957) *********************** 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 135 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8119 (mp0) REVERT: A 683 HIS cc_start: 0.6999 (t-90) cc_final: 0.6408 (t-90) REVERT: A 765 PHE cc_start: 0.8380 (t80) cc_final: 0.7989 (t80) REVERT: C 234 LEU cc_start: 0.8787 (tp) cc_final: 0.8237 (mm) REVERT: E 497 ASP cc_start: 0.7445 (m-30) cc_final: 0.6705 (t0) REVERT: E 514 ASP cc_start: 0.8240 (t0) cc_final: 0.7894 (t0) REVERT: E 517 MET cc_start: 0.8864 (tpp) cc_final: 0.8630 (tpp) REVERT: G 68 MET cc_start: 0.7026 (mtm) cc_final: 0.6746 (mtp) REVERT: G 92 ARG cc_start: 0.8386 (mmm160) cc_final: 0.7972 (mmm-85) REVERT: G 140 GLU cc_start: 0.7903 (pm20) cc_final: 0.7633 (pm20) outliers start: 27 outliers final: 13 residues processed: 129 average time/residue: 0.1177 time to fit residues: 20.3497 Evaluate side-chains 108 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 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 13 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN 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 = 0.3799 r_free = 0.3799 target = 0.138452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104802 restraints weight = 13242.027| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.34 r_work: 0.3028 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8945 Z= 0.225 Angle : 0.619 11.360 12136 Z= 0.316 Chirality : 0.046 0.178 1393 Planarity : 0.004 0.044 1541 Dihedral : 5.470 54.999 1195 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.19 % Allowed : 9.47 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.26), residues: 1102 helix: 2.10 (0.30), residues: 294 sheet: -0.14 (0.40), residues: 201 loop : -0.86 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 275 TYR 0.013 0.001 TYR C 182 PHE 0.021 0.002 PHE A 766 TRP 0.014 0.001 TRP A 159 HIS 0.008 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 8934) covalent geometry : angle 0.60944 (12114) SS BOND : bond 0.00895 ( 11) SS BOND : angle 2.57957 ( 22) hydrogen bonds : bond 0.04426 ( 326) hydrogen bonds : angle 4.12526 ( 957) *********************** 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 136 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8220 (mp0) REVERT: A 279 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9140 (pp) REVERT: A 683 HIS cc_start: 0.6985 (t-90) cc_final: 0.6421 (t-90) REVERT: A 765 PHE cc_start: 0.8401 (t80) cc_final: 0.8025 (t80) REVERT: C 234 LEU cc_start: 0.8701 (tp) cc_final: 0.8178 (mm) REVERT: E 497 ASP cc_start: 0.7591 (m-30) cc_final: 0.6792 (t0) REVERT: E 514 ASP cc_start: 0.8286 (t0) cc_final: 0.7958 (t0) REVERT: E 517 MET cc_start: 0.8880 (tpp) cc_final: 0.8586 (tpp) REVERT: G 68 MET cc_start: 0.7136 (mtm) cc_final: 0.6875 (mtp) REVERT: G 99 GLU cc_start: 0.8408 (pp20) cc_final: 0.8095 (pp20) REVERT: G 112 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8781 (ttpp) REVERT: G 140 GLU cc_start: 0.7906 (pm20) cc_final: 0.7656 (pm20) outliers start: 31 outliers final: 20 residues processed: 128 average time/residue: 0.1091 time to fit residues: 19.1896 Evaluate side-chains 117 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 67 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 562 THR 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 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 90 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.3980 chunk 77 optimal weight: 0.3980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN C 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104782 restraints weight = 13462.287| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.46 r_work: 0.2980 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8945 Z= 0.105 Angle : 0.535 6.905 12136 Z= 0.269 Chirality : 0.042 0.151 1393 Planarity : 0.003 0.035 1541 Dihedral : 5.107 58.494 1195 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.78 % Allowed : 11.53 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.26), residues: 1102 helix: 2.14 (0.30), residues: 296 sheet: -0.14 (0.40), residues: 201 loop : -0.76 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 92 TYR 0.011 0.001 TYR C 182 PHE 0.012 0.001 PHE A 706 TRP 0.009 0.001 TRP A 159 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8934) covalent geometry : angle 0.53204 (12114) SS BOND : bond 0.00482 ( 11) SS BOND : angle 1.40533 ( 22) hydrogen bonds : bond 0.03597 ( 326) hydrogen bonds : angle 3.95636 ( 957) *********************** 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: 27 poor density : 107 time to evaluate : 0.300 Fit side-chains REVERT: A 146 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8106 (mp0) REVERT: A 598 ASP cc_start: 0.9333 (OUTLIER) cc_final: 0.8782 (t0) REVERT: A 683 HIS cc_start: 0.7024 (t-90) cc_final: 0.6453 (t-90) REVERT: A 766 PHE cc_start: 0.8200 (m-10) cc_final: 0.7991 (m-10) REVERT: C 234 LEU cc_start: 0.8662 (tp) cc_final: 0.8133 (mm) REVERT: E 497 ASP cc_start: 0.7516 (m-30) cc_final: 0.6749 (t0) REVERT: E 514 ASP cc_start: 0.8164 (t0) cc_final: 0.7872 (t0) REVERT: G 68 MET cc_start: 0.6952 (mtm) cc_final: 0.6687 (mtp) REVERT: G 99 GLU cc_start: 0.8418 (pp20) cc_final: 0.8185 (pp20) REVERT: G 112 LYS cc_start: 0.9041 (ttpp) cc_final: 0.8769 (ttpp) REVERT: G 135 LEU cc_start: 0.7718 (tp) cc_final: 0.7437 (tt) REVERT: G 140 GLU cc_start: 0.7874 (pm20) cc_final: 0.7569 (pm20) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 0.1073 time to fit residues: 18.4719 Evaluate side-chains 119 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 271 ASN Chi-restraints excluded: chain A residue 344 MET 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 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 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 118 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 0.0070 chunk 62 optimal weight: 0.3980 chunk 28 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.136373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102889 restraints weight = 13292.188| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.58 r_work: 0.2958 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 0.116 8945 Z= 0.153 Angle : 0.577 14.076 12136 Z= 0.293 Chirality : 0.044 0.193 1393 Planarity : 0.003 0.034 1541 Dihedral : 5.194 57.370 1194 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.09 % Allowed : 11.53 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.27), residues: 1102 helix: 2.09 (0.30), residues: 294 sheet: -0.15 (0.40), residues: 201 loop : -0.79 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.012 0.001 TYR C 182 PHE 0.023 0.001 PHE A 754 TRP 0.011 0.001 TRP A 159 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8934) covalent geometry : angle 0.56282 (12114) SS BOND : bond 0.01154 ( 11) SS BOND : angle 3.08191 ( 22) hydrogen bonds : bond 0.03838 ( 326) hydrogen bonds : angle 4.03241 ( 957) *********************** 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 131 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8191 (mp0) REVERT: A 279 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9113 (pp) REVERT: A 598 ASP cc_start: 0.9342 (OUTLIER) cc_final: 0.9097 (t0) REVERT: A 683 HIS cc_start: 0.7033 (t-90) cc_final: 0.6434 (t-90) REVERT: C 167 GLN cc_start: 0.7309 (mm110) cc_final: 0.7047 (mm-40) REVERT: C 234 LEU cc_start: 0.8684 (tp) cc_final: 0.8156 (mm) REVERT: E 497 ASP cc_start: 0.7587 (m-30) cc_final: 0.6749 (t0) REVERT: G 68 MET cc_start: 0.6980 (mtm) cc_final: 0.6703 (mtp) REVERT: G 112 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8786 (ttpp) REVERT: G 140 GLU cc_start: 0.7795 (pm20) cc_final: 0.7544 (pm20) outliers start: 30 outliers final: 19 residues processed: 122 average time/residue: 0.1123 time to fit residues: 18.6281 Evaluate side-chains 119 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 173 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain G residue 90 MET 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 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106568 restraints weight = 13390.155| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.52 r_work: 0.3036 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8945 Z= 0.161 Angle : 0.585 11.636 12136 Z= 0.296 Chirality : 0.044 0.155 1393 Planarity : 0.003 0.035 1541 Dihedral : 5.255 57.716 1194 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.99 % Allowed : 12.15 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.26), residues: 1102 helix: 2.02 (0.30), residues: 294 sheet: -0.22 (0.39), residues: 207 loop : -0.80 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 92 TYR 0.012 0.001 TYR C 182 PHE 0.020 0.001 PHE A 765 TRP 0.011 0.001 TRP A 159 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8934) covalent geometry : angle 0.57449 (12114) SS BOND : bond 0.00914 ( 11) SS BOND : angle 2.62499 ( 22) hydrogen bonds : bond 0.03958 ( 326) hydrogen bonds : angle 4.10063 ( 957) *********************** 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 126 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.358 Fit side-chains REVERT: A 146 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8223 (mp0) REVERT: A 598 ASP cc_start: 0.9340 (OUTLIER) cc_final: 0.9088 (t0) REVERT: A 683 HIS cc_start: 0.7021 (t-90) cc_final: 0.6432 (t-90) REVERT: C 167 GLN cc_start: 0.7368 (mm110) cc_final: 0.7083 (mm-40) REVERT: C 234 LEU cc_start: 0.8600 (tp) cc_final: 0.8081 (mm) REVERT: E 497 ASP cc_start: 0.7666 (m-30) cc_final: 0.6850 (t0) REVERT: G 68 MET cc_start: 0.6956 (mtm) cc_final: 0.6673 (mtp) REVERT: G 99 GLU cc_start: 0.8387 (pp20) cc_final: 0.8154 (pp20) REVERT: G 112 LYS cc_start: 0.9010 (ttpp) cc_final: 0.8739 (ttpp) REVERT: G 135 LEU cc_start: 0.7700 (tp) cc_final: 0.7379 (tt) REVERT: G 140 GLU cc_start: 0.7727 (pm20) cc_final: 0.7494 (pm20) outliers start: 29 outliers final: 20 residues processed: 117 average time/residue: 0.1094 time to fit residues: 17.4781 Evaluate side-chains 118 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 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 90 MET 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 110 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105415 restraints weight = 13539.015| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.69 r_work: 0.3007 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8945 Z= 0.172 Angle : 0.591 9.412 12136 Z= 0.299 Chirality : 0.045 0.219 1393 Planarity : 0.003 0.035 1541 Dihedral : 5.337 58.019 1194 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.30 % Allowed : 11.74 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.27), residues: 1102 helix: 1.94 (0.30), residues: 294 sheet: -0.30 (0.39), residues: 209 loop : -0.81 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.015 0.001 TYR E 504 PHE 0.013 0.001 PHE A 808 TRP 0.012 0.001 TRP A 159 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8934) covalent geometry : angle 0.58370 (12114) SS BOND : bond 0.00683 ( 11) SS BOND : angle 2.21898 ( 22) hydrogen bonds : bond 0.04052 ( 326) hydrogen bonds : angle 4.15005 ( 957) *********************** 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: 32 poor density : 102 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8285 (mp0) REVERT: A 683 HIS cc_start: 0.6962 (t-90) cc_final: 0.6387 (t-90) REVERT: C 167 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7187 (mm-40) REVERT: C 234 LEU cc_start: 0.8592 (tp) cc_final: 0.8067 (mm) REVERT: E 497 ASP cc_start: 0.7648 (m-30) cc_final: 0.6773 (t0) REVERT: G 68 MET cc_start: 0.7002 (mtm) cc_final: 0.6706 (mtp) REVERT: G 99 GLU cc_start: 0.8384 (pp20) cc_final: 0.8074 (pp20) REVERT: G 112 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8796 (ttpp) REVERT: G 135 LEU cc_start: 0.7722 (tp) cc_final: 0.7420 (tt) REVERT: G 140 GLU cc_start: 0.7777 (pm20) cc_final: 0.7536 (pm20) outliers start: 32 outliers final: 21 residues processed: 125 average time/residue: 0.0995 time to fit residues: 17.3119 Evaluate side-chains 119 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 562 THR Chi-restraints excluded: chain A residue 570 LEU 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 236 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 107 LYS 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 1 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 106 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 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.138912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104735 restraints weight = 13232.259| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.52 r_work: 0.3039 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 8945 Z= 0.156 Angle : 0.603 11.578 12136 Z= 0.308 Chirality : 0.045 0.231 1393 Planarity : 0.003 0.035 1541 Dihedral : 5.302 58.817 1194 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.27), residues: 1102 helix: 1.92 (0.30), residues: 294 sheet: -0.31 (0.39), residues: 209 loop : -0.79 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 92 TYR 0.012 0.001 TYR C 182 PHE 0.020 0.001 PHE A 765 TRP 0.011 0.001 TRP A 159 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8934) covalent geometry : angle 0.59315 (12114) SS BOND : bond 0.01205 ( 11) SS BOND : angle 2.58628 ( 22) hydrogen bonds : bond 0.03971 ( 326) hydrogen bonds : angle 4.17310 ( 957) *********************** 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 125 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.386 Fit side-chains REVERT: A 683 HIS cc_start: 0.6930 (t-90) cc_final: 0.6369 (t-90) REVERT: C 167 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7136 (mm-40) REVERT: C 234 LEU cc_start: 0.8594 (tp) cc_final: 0.8074 (mm) REVERT: E 497 ASP cc_start: 0.7612 (m-30) cc_final: 0.6762 (t0) REVERT: E 504 TYR cc_start: 0.8326 (m-80) cc_final: 0.8041 (m-80) REVERT: G 68 MET cc_start: 0.6981 (mtm) cc_final: 0.6675 (mtp) REVERT: G 99 GLU cc_start: 0.8346 (pp20) cc_final: 0.8033 (pp20) REVERT: G 102 ASP cc_start: 0.9027 (t0) cc_final: 0.8602 (t0) REVERT: G 112 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8822 (ttpp) REVERT: G 135 LEU cc_start: 0.7693 (tp) cc_final: 0.7408 (tt) REVERT: G 140 GLU cc_start: 0.7748 (pm20) cc_final: 0.7519 (pm20) outliers start: 24 outliers final: 19 residues processed: 119 average time/residue: 0.1062 time to fit residues: 17.2981 Evaluate side-chains 115 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 562 THR 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 E residue 511 LYS Chi-restraints excluded: chain G residue 107 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 11 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.140403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107032 restraints weight = 13252.445| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.56 r_work: 0.3045 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8945 Z= 0.143 Angle : 0.586 8.881 12136 Z= 0.298 Chirality : 0.045 0.218 1393 Planarity : 0.003 0.035 1541 Dihedral : 5.262 59.700 1194 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.16 % Allowed : 13.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.27), residues: 1102 helix: 2.02 (0.30), residues: 289 sheet: -0.30 (0.39), residues: 209 loop : -0.75 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 145 TYR 0.012 0.001 TYR C 182 PHE 0.012 0.001 PHE A 808 TRP 0.011 0.001 TRP A 159 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8934) covalent geometry : angle 0.58005 (12114) SS BOND : bond 0.00882 ( 11) SS BOND : angle 2.07700 ( 22) hydrogen bonds : bond 0.03847 ( 326) hydrogen bonds : angle 4.15077 ( 957) *********************** 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 120 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.378 Fit side-chains REVERT: A 683 HIS cc_start: 0.6873 (t-90) cc_final: 0.6352 (t-90) REVERT: C 120 TRP cc_start: 0.7244 (p-90) cc_final: 0.6739 (p-90) REVERT: C 167 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7115 (mm-40) REVERT: C 234 LEU cc_start: 0.8577 (tp) cc_final: 0.8054 (mm) REVERT: E 497 ASP cc_start: 0.7683 (m-30) cc_final: 0.6807 (t0) REVERT: E 504 TYR cc_start: 0.8262 (m-80) cc_final: 0.8024 (m-80) REVERT: G 68 MET cc_start: 0.7014 (mtm) cc_final: 0.6725 (mtp) REVERT: G 99 GLU cc_start: 0.8367 (pp20) cc_final: 0.8061 (pp20) REVERT: G 102 ASP cc_start: 0.9026 (t0) cc_final: 0.8605 (t0) REVERT: G 112 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8800 (ttpp) REVERT: G 135 LEU cc_start: 0.7660 (tp) cc_final: 0.7355 (tt) REVERT: G 140 GLU cc_start: 0.7729 (pm20) cc_final: 0.7493 (pm20) outliers start: 21 outliers final: 19 residues processed: 114 average time/residue: 0.1087 time to fit residues: 16.6878 Evaluate side-chains 116 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 E residue 511 LYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 107 LYS 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 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106259 restraints weight = 13300.259| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.35 r_work: 0.3045 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8945 Z= 0.166 Angle : 0.599 7.303 12136 Z= 0.305 Chirality : 0.045 0.216 1393 Planarity : 0.003 0.035 1541 Dihedral : 5.390 58.607 1194 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.06 % Allowed : 14.01 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.27), residues: 1102 helix: 1.92 (0.30), residues: 294 sheet: -0.30 (0.39), residues: 209 loop : -0.81 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 92 TYR 0.012 0.001 TYR E 504 PHE 0.021 0.001 PHE A 765 TRP 0.012 0.001 TRP A 159 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8934) covalent geometry : angle 0.59472 (12114) SS BOND : bond 0.00779 ( 11) SS BOND : angle 1.76654 ( 22) hydrogen bonds : bond 0.04046 ( 326) hydrogen bonds : angle 4.19902 ( 957) ********************** 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 121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8680 (ptt90) REVERT: A 683 HIS cc_start: 0.6943 (t-90) cc_final: 0.6410 (t-90) REVERT: C 120 TRP cc_start: 0.7277 (p-90) cc_final: 0.6782 (p-90) REVERT: C 167 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7119 (mm-40) REVERT: C 234 LEU cc_start: 0.8498 (tp) cc_final: 0.7994 (mm) REVERT: E 497 ASP cc_start: 0.7608 (m-30) cc_final: 0.6803 (t0) REVERT: E 504 TYR cc_start: 0.8311 (m-80) cc_final: 0.8039 (m-80) REVERT: G 68 MET cc_start: 0.6994 (mtm) cc_final: 0.6706 (mtp) REVERT: G 99 GLU cc_start: 0.8362 (pp20) cc_final: 0.8069 (pp20) REVERT: G 102 ASP cc_start: 0.9016 (t0) cc_final: 0.8603 (t0) REVERT: G 112 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8822 (ttpp) REVERT: G 140 GLU cc_start: 0.7676 (pm20) cc_final: 0.7424 (pm20) outliers start: 20 outliers final: 19 residues processed: 116 average time/residue: 0.1083 time to fit residues: 17.2409 Evaluate side-chains 120 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 195 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 107 LYS 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 59 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 7 optimal weight: 0.0070 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103527 restraints weight = 13148.016| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.35 r_work: 0.2991 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8945 Z= 0.124 Angle : 0.578 7.186 12136 Z= 0.292 Chirality : 0.044 0.215 1393 Planarity : 0.003 0.036 1541 Dihedral : 5.180 57.049 1194 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.16 % Allowed : 14.01 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.27), residues: 1102 helix: 2.08 (0.30), residues: 289 sheet: -0.27 (0.38), residues: 209 loop : -0.74 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 202 TYR 0.011 0.001 TYR C 182 PHE 0.022 0.001 PHE A 754 TRP 0.010 0.001 TRP A 159 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8934) covalent geometry : angle 0.57089 (12114) SS BOND : bond 0.00656 ( 11) SS BOND : angle 2.25354 ( 22) hydrogen bonds : bond 0.03693 ( 326) hydrogen bonds : angle 4.11073 ( 957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.09 seconds wall clock time: 46 minutes 32.36 seconds (2792.36 seconds total)