Starting phenix.real_space_refine on Tue Feb 3 17:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmr_61611/02_2026/9jmr_61611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmr_61611/02_2026/9jmr_61611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jmr_61611/02_2026/9jmr_61611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmr_61611/02_2026/9jmr_61611.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmr_61611/02_2026/9jmr_61611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmr_61611/02_2026/9jmr_61611.cif" } resolution = 2.78 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= 0.025 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 15 5.16 5 C 3624 2.51 5 N 988 2.21 5 O 1064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5691 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3986 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 521} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'TYR:plan': 4, 'GLU:plan': 17, 'GLN:plan1': 4, 'ARG:plan': 18, 'ASP:plan': 12, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 264 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 926 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 779 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 1.54, per 1000 atoms: 0.27 Number of scatterers: 5691 At special positions: 0 Unit cell: (77.35, 124.8, 169, 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 15 16.00 O 1064 8.00 N 988 7.00 C 3624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 424 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 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: 0.42 Conformation dependent library (CDL) restraints added in 498.8 milliseconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 14 sheets defined 16.7% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.598A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.755A pdb=" N ARG A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.631A pdb=" N ALA A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 570 removed outlier: 3.667A pdb=" N HIS A 544 " --> pdb=" O HIS A 540 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 561 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.538A pdb=" N ARG A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.722A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.937A pdb=" N LYS H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.853A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.816A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AA2, first strand: chain 'A' and resid 377 through 383 removed outlier: 4.408A pdb=" N LEU A 160 " --> pdb=" O TRP A 380 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLU A 382 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA A 158 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 15.409A pdb=" N PHE A 153 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N SER A 470 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU A 155 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 405 through 409 removed outlier: 15.409A pdb=" N PHE A 153 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N SER A 470 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU A 155 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 202 removed outlier: 5.406A pdb=" N ILE A 193 " --> pdb=" O TRP A 185 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TRP A 185 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 273 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.888A pdb=" N PHE A 273 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LYS A 171 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A 366 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL A 351 " --> pdb=" O HIS A 335 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS A 335 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 219 Processing sheet with id=AA7, first strand: chain 'A' and resid 221 through 226 Processing sheet with id=AA8, first strand: chain 'A' and resid 667 through 669 removed outlier: 3.788A pdb=" N PHE A 667 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 683 " --> pdb=" O TYR A 675 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.903A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.765A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.237A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.801A pdb=" N GLN L 36 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.529A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 678 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: 1.01 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1370 1.33 - 1.45: 1333 1.45 - 1.57: 3107 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 5830 Sorted by residual: bond pdb=" CA SER L 12 " pdb=" CB SER L 12 " ideal model delta sigma weight residual 1.527 1.488 0.039 1.30e-02 5.92e+03 9.18e+00 bond pdb=" CA SER L 5 " pdb=" CB SER L 5 " ideal model delta sigma weight residual 1.527 1.487 0.040 1.38e-02 5.25e+03 8.37e+00 bond pdb=" N LEU L 11 " pdb=" CA LEU L 11 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.00e+00 bond pdb=" N LEU A 655 " pdb=" CA LEU A 655 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.57e+00 bond pdb=" CA SER L 14 " pdb=" CB SER L 14 " ideal model delta sigma weight residual 1.534 1.491 0.043 1.57e-02 4.06e+03 7.52e+00 ... (remaining 5825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 7673 2.10 - 4.20: 256 4.20 - 6.30: 26 6.30 - 8.41: 7 8.41 - 10.51: 3 Bond angle restraints: 7965 Sorted by residual: angle pdb=" N ILE A 436 " pdb=" CA ILE A 436 " pdb=" C ILE A 436 " ideal model delta sigma weight residual 113.47 107.98 5.49 1.01e+00 9.80e-01 2.96e+01 angle pdb=" O SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 121.32 115.44 5.88 1.15e+00 7.56e-01 2.62e+01 angle pdb=" C ALA L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" N ILE A 656 " pdb=" CA ILE A 656 " pdb=" C ILE A 656 " ideal model delta sigma weight residual 112.80 107.70 5.10 1.15e+00 7.56e-01 1.96e+01 angle pdb=" C THR A 264 " pdb=" CA THR A 264 " pdb=" CB THR A 264 " ideal model delta sigma weight residual 111.22 117.50 -6.28 1.72e+00 3.38e-01 1.33e+01 ... (remaining 7960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 3268 15.57 - 31.14: 101 31.14 - 46.71: 21 46.71 - 62.28: 3 62.28 - 77.85: 4 Dihedral angle restraints: 3397 sinusoidal: 1140 harmonic: 2257 Sorted by residual: dihedral pdb=" CB CYS A 375 " pdb=" SG CYS A 375 " pdb=" SG CYS A 424 " pdb=" CB CYS A 424 " ideal model delta sinusoidal sigma weight residual 93.00 166.99 -73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CA SER A 652 " pdb=" C SER A 652 " pdb=" N ARG A 653 " pdb=" CA ARG A 653 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA GLN A 611 " pdb=" C GLN A 611 " pdb=" N ASN A 612 " pdb=" CA ASN A 612 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 3394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 632 0.054 - 0.108: 209 0.108 - 0.162: 40 0.162 - 0.216: 13 0.216 - 0.270: 4 Chirality restraints: 898 Sorted by residual: chirality pdb=" CB ILE A 157 " pdb=" CA ILE A 157 " pdb=" CG1 ILE A 157 " pdb=" CG2 ILE A 157 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE A 323 " pdb=" CA ILE A 323 " pdb=" CG1 ILE A 323 " pdb=" CG2 ILE A 323 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 895 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 7 " -0.031 2.00e-02 2.50e+03 5.86e-02 3.44e+01 pdb=" C SER L 7 " 0.101 2.00e-02 2.50e+03 pdb=" O SER L 7 " -0.035 2.00e-02 2.50e+03 pdb=" N PRO L 8 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 35 " -0.009 2.00e-02 2.50e+03 2.40e-02 8.63e+00 pdb=" CG HIS H 35 " 0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS H 35 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS H 35 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS H 35 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS H 35 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 50 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C THR L 50 " 0.041 2.00e-02 2.50e+03 pdb=" O THR L 50 " -0.015 2.00e-02 2.50e+03 pdb=" N SER L 51 " -0.014 2.00e-02 2.50e+03 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1279 2.79 - 3.31: 4385 3.31 - 3.84: 8856 3.84 - 4.37: 9780 4.37 - 4.90: 17633 Nonbonded interactions: 41933 Sorted by model distance: nonbonded pdb=" CD1 ILE L 2 " pdb=" CD2 TYR L 92 " model vdw 2.258 3.760 nonbonded pdb=" NH1 ARG A 315 " pdb=" O TRP L 90 " model vdw 2.320 3.120 nonbonded pdb=" O GLU A 677 " pdb=" OG SER A 680 " model vdw 2.354 3.040 nonbonded pdb=" OD1 ASP H 73 " pdb=" OG1 THR H 78 " model vdw 2.372 3.040 nonbonded pdb=" OG1 THR A 358 " pdb=" O PHE A 361 " model vdw 2.372 3.040 ... (remaining 41928 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: 11.820 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.780 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.006 0.053 5835 Z= 0.314 Angle : 0.876 10.508 7975 Z= 0.516 Chirality : 0.059 0.270 898 Planarity : 0.007 0.059 1028 Dihedral : 9.047 77.845 1934 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.19 % Allowed : 2.65 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -3.17 (0.26), residues: 757 helix: -4.53 (0.23), residues: 91 sheet: -1.01 (0.30), residues: 245 loop : -2.24 (0.25), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 381 TYR 0.027 0.003 TYR H 50 PHE 0.025 0.003 PHE A 298 TRP 0.026 0.003 TRP H 112 HIS 0.035 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 5830) covalent geometry : angle 0.87435 ( 7965) SS BOND : bond 0.00401 ( 5) SS BOND : angle 1.57683 ( 10) hydrogen bonds : bond 0.25813 ( 222) hydrogen bonds : angle 10.45586 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 206 GLN cc_start: 0.7441 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 563 ASP cc_start: 0.6642 (m-30) cc_final: 0.6431 (m-30) REVERT: A 705 ARG cc_start: 0.7533 (mmt-90) cc_final: 0.7319 (ttp-170) REVERT: A 730 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8268 (tp40) outliers start: 1 outliers final: 1 residues processed: 170 average time/residue: 0.5196 time to fit residues: 92.3994 Evaluate side-chains 133 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 178 ASN A 542 GLN A 733 ASN A 734 GLN L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097723 restraints weight = 8159.760| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.86 r_work: 0.3108 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5835 Z= 0.235 Angle : 0.599 6.190 7975 Z= 0.325 Chirality : 0.046 0.141 898 Planarity : 0.006 0.081 1028 Dihedral : 4.949 22.729 845 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.98 % Allowed : 10.98 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -1.91 (0.28), residues: 757 helix: -2.12 (0.45), residues: 93 sheet: -0.37 (0.30), residues: 262 loop : -1.67 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 200 TYR 0.026 0.002 TYR A 437 PHE 0.021 0.002 PHE A 298 TRP 0.016 0.002 TRP H 112 HIS 0.009 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 5830) covalent geometry : angle 0.59872 ( 7965) SS BOND : bond 0.00368 ( 5) SS BOND : angle 0.97818 ( 10) hydrogen bonds : bond 0.04821 ( 222) hydrogen bonds : angle 5.91227 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8786 (mtm-85) cc_final: 0.8534 (mtm-85) REVERT: A 418 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7500 (ttp-110) REVERT: A 563 ASP cc_start: 0.7353 (m-30) cc_final: 0.7139 (m-30) REVERT: A 705 ARG cc_start: 0.8173 (mmt-90) cc_final: 0.7495 (ttp-170) REVERT: A 715 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8400 (mtp-110) REVERT: A 730 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8529 (tp40) outliers start: 21 outliers final: 6 residues processed: 144 average time/residue: 0.5513 time to fit residues: 82.9430 Evaluate side-chains 131 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097623 restraints weight = 8053.077| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.84 r_work: 0.3104 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5835 Z= 0.178 Angle : 0.549 6.734 7975 Z= 0.293 Chirality : 0.045 0.156 898 Planarity : 0.005 0.056 1028 Dihedral : 4.566 21.035 844 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.22 % Allowed : 12.69 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -1.21 (0.29), residues: 757 helix: -0.42 (0.54), residues: 93 sheet: 0.00 (0.30), residues: 262 loop : -1.46 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 373 TYR 0.026 0.002 TYR A 437 PHE 0.019 0.002 PHE A 298 TRP 0.011 0.002 TRP L 90 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5830) covalent geometry : angle 0.54841 ( 7965) SS BOND : bond 0.00337 ( 5) SS BOND : angle 0.81330 ( 10) hydrogen bonds : bond 0.04066 ( 222) hydrogen bonds : angle 5.36838 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.233 Fit side-chains REVERT: A 418 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7538 (ttp-110) REVERT: A 563 ASP cc_start: 0.7349 (m-30) cc_final: 0.7134 (m-30) REVERT: A 705 ARG cc_start: 0.8190 (mmt-90) cc_final: 0.7556 (ttp-170) REVERT: A 715 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8395 (mtp-110) REVERT: A 730 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8514 (tp40) outliers start: 17 outliers final: 9 residues processed: 132 average time/residue: 0.5460 time to fit residues: 75.3799 Evaluate side-chains 134 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 HIS A 733 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098103 restraints weight = 8033.017| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.86 r_work: 0.3107 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5835 Z= 0.144 Angle : 0.524 6.993 7975 Z= 0.276 Chirality : 0.044 0.153 898 Planarity : 0.004 0.047 1028 Dihedral : 4.296 21.839 844 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.46 % Allowed : 14.58 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -0.79 (0.30), residues: 757 helix: 0.34 (0.56), residues: 93 sheet: 0.20 (0.30), residues: 262 loop : -1.24 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 315 TYR 0.027 0.002 TYR A 437 PHE 0.017 0.001 PHE A 298 TRP 0.012 0.001 TRP L 90 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5830) covalent geometry : angle 0.52390 ( 7965) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.70652 ( 10) hydrogen bonds : bond 0.03569 ( 222) hydrogen bonds : angle 5.09306 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.232 Fit side-chains REVERT: A 334 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8109 (mt-10) REVERT: A 396 PHE cc_start: 0.7845 (m-80) cc_final: 0.7487 (m-80) REVERT: A 418 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7529 (ttp-110) REVERT: A 705 ARG cc_start: 0.8182 (mmt-90) cc_final: 0.7547 (ttp-170) REVERT: A 730 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8511 (tp40) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.6079 time to fit residues: 82.9843 Evaluate side-chains 136 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 0.0570 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 733 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097888 restraints weight = 8164.238| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.87 r_work: 0.3113 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5835 Z= 0.155 Angle : 0.530 7.131 7975 Z= 0.279 Chirality : 0.044 0.155 898 Planarity : 0.004 0.050 1028 Dihedral : 4.253 21.032 844 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.65 % Allowed : 14.20 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -0.50 (0.30), residues: 757 helix: 0.72 (0.57), residues: 93 sheet: 0.47 (0.31), residues: 254 loop : -1.13 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.026 0.002 TYR A 437 PHE 0.017 0.001 PHE A 298 TRP 0.010 0.001 TRP L 90 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5830) covalent geometry : angle 0.52690 ( 7965) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.81147 ( 10) hydrogen bonds : bond 0.03579 ( 222) hydrogen bonds : angle 5.03568 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.222 Fit side-chains REVERT: A 396 PHE cc_start: 0.7908 (m-80) cc_final: 0.7574 (m-80) REVERT: A 418 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7524 (ttp-110) REVERT: A 705 ARG cc_start: 0.8192 (mmt-90) cc_final: 0.7601 (ttp-170) outliers start: 14 outliers final: 10 residues processed: 131 average time/residue: 0.5136 time to fit residues: 70.2726 Evaluate side-chains 135 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN A 734 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097969 restraints weight = 8090.325| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.87 r_work: 0.3115 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5835 Z= 0.144 Angle : 0.516 6.812 7975 Z= 0.271 Chirality : 0.044 0.139 898 Planarity : 0.004 0.046 1028 Dihedral : 4.169 21.150 844 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.46 % Allowed : 15.72 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -0.33 (0.30), residues: 757 helix: 0.86 (0.57), residues: 94 sheet: 0.60 (0.32), residues: 253 loop : -1.03 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 381 TYR 0.027 0.002 TYR A 437 PHE 0.017 0.001 PHE A 298 TRP 0.011 0.001 TRP L 90 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5830) covalent geometry : angle 0.51403 ( 7965) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.38454 ( 10) hydrogen bonds : bond 0.03457 ( 222) hydrogen bonds : angle 4.96977 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.209 Fit side-chains REVERT: A 396 PHE cc_start: 0.7970 (m-80) cc_final: 0.7732 (m-80) REVERT: A 413 GLN cc_start: 0.7799 (tp40) cc_final: 0.7553 (mm-40) REVERT: A 418 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7524 (ttp-110) REVERT: A 705 ARG cc_start: 0.8181 (mmt-90) cc_final: 0.7625 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.5190 time to fit residues: 70.9806 Evaluate side-chains 139 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097488 restraints weight = 8127.432| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.85 r_work: 0.3109 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5835 Z= 0.171 Angle : 0.538 6.960 7975 Z= 0.283 Chirality : 0.044 0.133 898 Planarity : 0.005 0.057 1028 Dihedral : 4.276 21.296 844 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.41 % Allowed : 15.34 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -0.26 (0.30), residues: 757 helix: 0.94 (0.57), residues: 94 sheet: 0.64 (0.32), residues: 252 loop : -0.99 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 373 TYR 0.027 0.002 TYR A 437 PHE 0.018 0.002 PHE A 298 TRP 0.011 0.001 TRP L 90 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5830) covalent geometry : angle 0.53621 ( 7965) SS BOND : bond 0.00314 ( 5) SS BOND : angle 1.23084 ( 10) hydrogen bonds : bond 0.03643 ( 222) hydrogen bonds : angle 5.03695 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.204 Fit side-chains REVERT: A 418 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7536 (ttp-110) REVERT: A 421 LEU cc_start: 0.8527 (mt) cc_final: 0.8283 (mp) REVERT: A 705 ARG cc_start: 0.8190 (mmt-90) cc_final: 0.7630 (ttp-170) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.4722 time to fit residues: 67.0770 Evaluate side-chains 145 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 0.0370 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098341 restraints weight = 8013.433| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.83 r_work: 0.3123 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5835 Z= 0.132 Angle : 0.515 7.258 7975 Z= 0.269 Chirality : 0.043 0.132 898 Planarity : 0.004 0.045 1028 Dihedral : 4.123 20.939 844 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.84 % Allowed : 15.91 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -0.17 (0.31), residues: 757 helix: 1.01 (0.58), residues: 95 sheet: 0.64 (0.32), residues: 253 loop : -0.88 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 373 TYR 0.027 0.002 TYR A 437 PHE 0.016 0.001 PHE A 298 TRP 0.011 0.001 TRP L 90 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5830) covalent geometry : angle 0.51354 ( 7965) SS BOND : bond 0.00292 ( 5) SS BOND : angle 1.02664 ( 10) hydrogen bonds : bond 0.03354 ( 222) hydrogen bonds : angle 4.91330 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.258 Fit side-chains REVERT: A 418 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7521 (ttp-110) REVERT: A 421 LEU cc_start: 0.8505 (mt) cc_final: 0.8257 (mp) REVERT: A 705 ARG cc_start: 0.8183 (mmt-90) cc_final: 0.7636 (ttp-170) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.4327 time to fit residues: 58.9478 Evaluate side-chains 134 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 0.0870 chunk 72 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 733 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.099773 restraints weight = 8084.646| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.87 r_work: 0.3147 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5835 Z= 0.089 Angle : 0.485 7.077 7975 Z= 0.253 Chirality : 0.042 0.132 898 Planarity : 0.004 0.041 1028 Dihedral : 3.795 19.841 844 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.08 % Allowed : 16.86 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 0.02 (0.31), residues: 757 helix: 1.38 (0.59), residues: 95 sheet: 0.74 (0.32), residues: 253 loop : -0.79 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 373 TYR 0.021 0.001 TYR A 437 PHE 0.013 0.001 PHE A 298 TRP 0.011 0.001 TRP L 90 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 5830) covalent geometry : angle 0.48479 ( 7965) SS BOND : bond 0.00288 ( 5) SS BOND : angle 0.84379 ( 10) hydrogen bonds : bond 0.02914 ( 222) hydrogen bonds : angle 4.66151 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.135 Fit side-chains REVERT: A 206 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 221 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7796 (tttm) REVERT: A 418 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7510 (ttp-110) REVERT: A 421 LEU cc_start: 0.8480 (mt) cc_final: 0.8228 (mp) REVERT: A 705 ARG cc_start: 0.8188 (mmt-90) cc_final: 0.7476 (ttt180) outliers start: 11 outliers final: 9 residues processed: 131 average time/residue: 0.4602 time to fit residues: 63.1666 Evaluate side-chains 134 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 55 optimal weight: 0.0010 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 733 ASN A 734 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099070 restraints weight = 8143.310| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.87 r_work: 0.3133 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5835 Z= 0.119 Angle : 0.500 7.491 7975 Z= 0.263 Chirality : 0.043 0.132 898 Planarity : 0.004 0.042 1028 Dihedral : 3.945 20.194 844 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.70 % Allowed : 17.42 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 0.00 (0.31), residues: 757 helix: 1.47 (0.58), residues: 95 sheet: 0.68 (0.32), residues: 252 loop : -0.80 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 373 TYR 0.021 0.001 TYR A 437 PHE 0.015 0.001 PHE A 298 TRP 0.010 0.001 TRP L 90 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5830) covalent geometry : angle 0.49941 ( 7965) SS BOND : bond 0.00298 ( 5) SS BOND : angle 0.94245 ( 10) hydrogen bonds : bond 0.03216 ( 222) hydrogen bonds : angle 4.74672 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.127 Fit side-chains REVERT: A 221 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7809 (tttm) REVERT: A 418 ARG cc_start: 0.7765 (ttp-110) cc_final: 0.7534 (ttp-110) REVERT: A 421 LEU cc_start: 0.8502 (mt) cc_final: 0.8252 (mp) REVERT: A 705 ARG cc_start: 0.8179 (mmt-90) cc_final: 0.7491 (ttt180) outliers start: 9 outliers final: 8 residues processed: 129 average time/residue: 0.4653 time to fit residues: 62.7079 Evaluate side-chains 133 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.118164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097225 restraints weight = 8000.897| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.85 r_work: 0.3104 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5835 Z= 0.202 Angle : 0.557 7.989 7975 Z= 0.295 Chirality : 0.045 0.132 898 Planarity : 0.005 0.064 1028 Dihedral : 4.340 21.008 844 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.70 % Allowed : 17.23 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: -0.13 (0.30), residues: 757 helix: 1.24 (0.57), residues: 95 sheet: 0.60 (0.32), residues: 248 loop : -0.83 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 373 TYR 0.025 0.002 TYR A 437 PHE 0.020 0.002 PHE A 298 TRP 0.011 0.002 TRP L 90 HIS 0.003 0.001 HIS A 736 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 5830) covalent geometry : angle 0.55643 ( 7965) SS BOND : bond 0.00304 ( 5) SS BOND : angle 1.07234 ( 10) hydrogen bonds : bond 0.03847 ( 222) hydrogen bonds : angle 5.06415 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.24 seconds wall clock time: 49 minutes 38.55 seconds (2978.55 seconds total)