Starting phenix.real_space_refine on Tue Sep 24 15:34:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/09_2024/8h8b_34541.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/09_2024/8h8b_34541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/09_2024/8h8b_34541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/09_2024/8h8b_34541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/09_2024/8h8b_34541.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/09_2024/8h8b_34541.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 13 5.16 5 C 5251 2.51 5 N 1439 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8344 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8344 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 24, 'TRANS': 1002} Time building chain proxies: 5.09, per 1000 atoms: 0.61 Number of scatterers: 8344 At special positions: 0 Unit cell: (76.56, 89.61, 119.19, 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 13 16.00 O 1641 8.00 N 1439 7.00 C 5251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 977.9 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 17 sheets defined 2.8% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.590A pdb=" N SER A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1112 Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'A' and resid 1154 through 1165 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 170 removed outlier: 6.677A pdb=" N TRP A 177 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207 removed outlier: 4.363A pdb=" N SER A 216 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 5.891A pdb=" N CYS A 247 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR A 258 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE A 249 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE A 256 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 251 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.503A pdb=" N ARG A 290 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 removed outlier: 7.072A pdb=" N VAL A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 305 " --> pdb=" O HIS A 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335 removed outlier: 3.665A pdb=" N ILE A 334 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 343 " --> pdb=" O ILE A 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.554A pdb=" N GLU A 376 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 402 removed outlier: 5.513A pdb=" N LEU A 428 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU A 449 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 470 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 481 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 491 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LYS A 502 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP A 514 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 544 through 547 removed outlier: 6.464A pdb=" N ARG A 544 " --> pdb=" O HIS A 556 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS A 556 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP A 546 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL A 554 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN A 574 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR A 595 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA A 621 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR A 662 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 696 through 697 removed outlier: 6.916A pdb=" N LYS A 696 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 717 removed outlier: 4.579A pdb=" N GLN A 724 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 726 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 758 through 763 removed outlier: 7.257A pdb=" N GLN A 758 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG A 770 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN A 760 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 762 " --> pdb=" O HIS A 766 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS A 766 " --> pdb=" O SER A 762 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 799 through 803 removed outlier: 6.049A pdb=" N ASP A 803 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 808 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N ARG A 807 " --> pdb=" O TYR A 825 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N TYR A 825 " --> pdb=" O ARG A 807 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER A 809 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 823 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A 832 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 853 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 852 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 918 through 919 removed outlier: 6.526A pdb=" N LYS A 918 " --> pdb=" O GLU A 925 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU A 925 " --> pdb=" O TYR A 932 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 961 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS A 971 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 983 " --> pdb=" O HIS A 971 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 973 " --> pdb=" O THR A 981 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR A 981 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A 991 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU A1002 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 993 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 998 " --> pdb=" O GLU A 995 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A1009 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A1042 " --> pdb=" O GLU A1033 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU A1041 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A1045 " --> pdb=" O ILE A1050 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A1050 " --> pdb=" O ASP A1045 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A1066 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER A1055 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A1064 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1013 through 1014 removed outlier: 6.205A pdb=" N ILE A1019 " --> pdb=" O GLN A1014 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1079 through 1081 removed outlier: 3.597A pdb=" N ARG A1100 " --> pdb=" O ASP A1095 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 582 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: 3.58 Time building geometry restraints manager: 2.38 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: 2083 1.46 - 1.58: 3641 1.58 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 8546 Sorted by residual: bond pdb=" CA GLU A 271 " pdb=" C GLU A 271 " ideal model delta sigma weight residual 1.519 1.529 -0.009 1.01e-02 9.80e+03 8.60e-01 bond pdb=" CA ILE A1019 " pdb=" CB ILE A1019 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" N THR A 332 " pdb=" CA THR A 332 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.42e-02 4.96e+03 6.85e-01 bond pdb=" N TYR A 242 " pdb=" CA TYR A 242 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.39e-02 5.18e+03 6.13e-01 bond pdb=" CA VAL A 735 " pdb=" C VAL A 735 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.01e-02 9.80e+03 5.14e-01 ... (remaining 8541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 11450 1.63 - 3.26: 100 3.26 - 4.88: 16 4.88 - 6.51: 3 6.51 - 8.14: 1 Bond angle restraints: 11570 Sorted by residual: angle pdb=" N CYS A 147 " pdb=" CA CYS A 147 " pdb=" C CYS A 147 " ideal model delta sigma weight residual 108.24 112.24 -4.00 1.32e+00 5.74e-01 9.20e+00 angle pdb=" C HIS A 302 " pdb=" N ASN A 303 " pdb=" CA ASN A 303 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.98e+00 angle pdb=" N SER A 216 " pdb=" CA SER A 216 " pdb=" C SER A 216 " ideal model delta sigma weight residual 108.32 112.95 -4.63 1.64e+00 3.72e-01 7.98e+00 angle pdb=" N ASP A 397 " pdb=" CA ASP A 397 " pdb=" C ASP A 397 " ideal model delta sigma weight residual 107.93 111.54 -3.61 1.65e+00 3.67e-01 4.80e+00 angle pdb=" CA VAL A 319 " pdb=" C VAL A 319 " pdb=" N GLU A 320 " ideal model delta sigma weight residual 116.60 119.55 -2.95 1.45e+00 4.76e-01 4.14e+00 ... (remaining 11565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4587 17.86 - 35.71: 329 35.71 - 53.57: 58 53.57 - 71.43: 18 71.43 - 89.29: 6 Dihedral angle restraints: 4998 sinusoidal: 2018 harmonic: 2980 Sorted by residual: dihedral pdb=" CA LYS A 304 " pdb=" C LYS A 304 " pdb=" N ARG A 305 " pdb=" CA ARG A 305 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CB GLU A 429 " pdb=" CG GLU A 429 " pdb=" CD GLU A 429 " pdb=" OE1 GLU A 429 " ideal model delta sinusoidal sigma weight residual 0.00 -89.29 89.29 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASN A 303 " pdb=" C ASN A 303 " pdb=" N LYS A 304 " pdb=" CA LYS A 304 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 4995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 705 0.027 - 0.054: 322 0.054 - 0.081: 61 0.081 - 0.108: 68 0.108 - 0.135: 30 Chirality restraints: 1186 Sorted by residual: chirality pdb=" CA THR A 332 " pdb=" N THR A 332 " pdb=" C THR A 332 " pdb=" CB THR A 332 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 726 " pdb=" N ILE A 726 " pdb=" C ILE A 726 " pdb=" CB ILE A 726 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE A 597 " pdb=" N ILE A 597 " pdb=" C ILE A 597 " pdb=" CB ILE A 597 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1183 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 251 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO A 252 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 453 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 454 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1014 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A1015 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A1015 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1015 " 0.016 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1165 2.76 - 3.30: 7163 3.30 - 3.83: 12974 3.83 - 4.37: 15555 4.37 - 4.90: 27797 Nonbonded interactions: 64654 Sorted by model distance: nonbonded pdb=" O SER A 587 " pdb=" OG1 THR A 595 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 742 " pdb=" O GLY A 745 " model vdw 2.246 3.040 nonbonded pdb=" O ILE A 871 " pdb=" OH TYR A 886 " model vdw 2.265 3.040 nonbonded pdb=" O THR A 796 " pdb=" OG SER A 814 " model vdw 2.287 3.040 nonbonded pdb=" O GLY A 938 " pdb=" OH TYR A1116 " model vdw 2.317 3.040 ... (remaining 64649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.160 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.001 0.016 8546 Z= 0.096 Angle : 0.457 8.138 11570 Z= 0.276 Chirality : 0.040 0.135 1186 Planarity : 0.002 0.037 1528 Dihedral : 12.997 89.286 3114 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.67 % Allowed : 6.86 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.23), residues: 1025 helix: -1.91 (1.51), residues: 12 sheet: -0.79 (0.37), residues: 188 loop : -2.52 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 438 HIS 0.004 0.000 HIS A 444 PHE 0.006 0.000 PHE A 267 TYR 0.009 0.001 TYR A 242 ARG 0.001 0.000 ARG A 979 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.916 Fit side-chains REVERT: A 226 GLU cc_start: 0.5483 (pt0) cc_final: 0.5206 (pt0) REVERT: A 228 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 403 GLU cc_start: 0.6716 (tp30) cc_final: 0.6347 (mm-30) REVERT: A 918 LYS cc_start: 0.7893 (tttt) cc_final: 0.7538 (tttp) REVERT: A 924 ILE cc_start: 0.8365 (mp) cc_final: 0.8132 (mt) outliers start: 6 outliers final: 3 residues processed: 166 average time/residue: 0.2500 time to fit residues: 54.3189 Evaluate side-chains 92 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 1170 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 421 HIS A 456 ASN A 529 HIS A 585 GLN A 622 GLN A 633 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 760 GLN A 772 GLN A 799 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN A 937 GLN A 959 GLN A1082 GLN A1089 ASN A1148 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8546 Z= 0.329 Angle : 0.681 15.361 11570 Z= 0.358 Chirality : 0.048 0.163 1186 Planarity : 0.005 0.044 1528 Dihedral : 5.049 31.029 1159 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 2.92 % Allowed : 10.91 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1025 helix: -1.19 (1.46), residues: 13 sheet: -0.27 (0.35), residues: 236 loop : -2.27 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 856 HIS 0.009 0.002 HIS A 556 PHE 0.027 0.002 PHE A1075 TYR 0.023 0.002 TYR A1094 ARG 0.004 0.001 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 0.960 Fit side-chains REVERT: A 228 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 487 LEU cc_start: 0.8555 (mm) cc_final: 0.8230 (mm) REVERT: A 783 ARG cc_start: 0.7775 (ptt90) cc_final: 0.7552 (ttp-110) REVERT: A 918 LYS cc_start: 0.8059 (tttt) cc_final: 0.7783 (ttmm) outliers start: 26 outliers final: 17 residues processed: 128 average time/residue: 0.1959 time to fit residues: 35.0421 Evaluate side-chains 99 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.0000 chunk 91 optimal weight: 0.7980 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 GLN A 937 GLN A1121 ASN A1160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8546 Z= 0.223 Angle : 0.602 14.308 11570 Z= 0.312 Chirality : 0.045 0.160 1186 Planarity : 0.004 0.042 1528 Dihedral : 4.830 31.120 1158 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 2.81 % Allowed : 13.39 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.25), residues: 1025 helix: -0.86 (1.49), residues: 13 sheet: -0.27 (0.34), residues: 249 loop : -2.04 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 177 HIS 0.005 0.001 HIS A 650 PHE 0.013 0.001 PHE A1075 TYR 0.014 0.001 TYR A1094 ARG 0.005 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.968 Fit side-chains REVERT: A 487 LEU cc_start: 0.8583 (mm) cc_final: 0.8259 (mm) REVERT: A 783 ARG cc_start: 0.7748 (ptt90) cc_final: 0.7534 (ttp-110) REVERT: A 918 LYS cc_start: 0.7896 (tttt) cc_final: 0.7641 (ttmm) outliers start: 25 outliers final: 19 residues processed: 106 average time/residue: 0.1766 time to fit residues: 27.1094 Evaluate side-chains 98 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1132 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8546 Z= 0.171 Angle : 0.575 13.895 11570 Z= 0.294 Chirality : 0.045 0.156 1186 Planarity : 0.003 0.042 1528 Dihedral : 4.651 34.315 1158 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 2.59 % Allowed : 14.51 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.25), residues: 1025 helix: -0.32 (1.58), residues: 13 sheet: -0.03 (0.35), residues: 247 loop : -1.96 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 177 HIS 0.004 0.001 HIS A 650 PHE 0.012 0.001 PHE A1075 TYR 0.013 0.001 TYR A1094 ARG 0.003 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.903 Fit side-chains REVERT: A 783 ARG cc_start: 0.7773 (ptt90) cc_final: 0.7570 (ttp-110) REVERT: A 918 LYS cc_start: 0.7821 (tttt) cc_final: 0.7557 (ttmm) REVERT: A 943 ARG cc_start: 0.7936 (tmm-80) cc_final: 0.7393 (ttp-170) outliers start: 23 outliers final: 16 residues processed: 103 average time/residue: 0.1809 time to fit residues: 26.8066 Evaluate side-chains 97 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 481 GLN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 8546 Z= 0.500 Angle : 0.776 16.780 11570 Z= 0.404 Chirality : 0.052 0.180 1186 Planarity : 0.005 0.049 1528 Dihedral : 5.910 35.689 1158 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 3.49 % Allowed : 15.97 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.25), residues: 1025 helix: -0.93 (1.36), residues: 12 sheet: -0.27 (0.35), residues: 244 loop : -2.11 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 513 HIS 0.009 0.002 HIS A 766 PHE 0.028 0.002 PHE A1075 TYR 0.018 0.002 TYR A1094 ARG 0.004 0.001 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.947 Fit side-chains REVERT: A 149 GLU cc_start: 0.6064 (pm20) cc_final: 0.5496 (pm20) REVERT: A 226 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6012 (pt0) REVERT: A 918 LYS cc_start: 0.7919 (tttt) cc_final: 0.7636 (ttmm) REVERT: A 943 ARG cc_start: 0.8055 (tmm-80) cc_final: 0.7557 (ttp-170) outliers start: 31 outliers final: 23 residues processed: 113 average time/residue: 0.1972 time to fit residues: 31.3655 Evaluate side-chains 99 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 481 GLN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8546 Z= 0.167 Angle : 0.591 14.014 11570 Z= 0.306 Chirality : 0.045 0.159 1186 Planarity : 0.003 0.047 1528 Dihedral : 4.951 34.165 1158 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.14 % Allowed : 18.45 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.25), residues: 1025 helix: -0.32 (1.55), residues: 13 sheet: -0.14 (0.35), residues: 249 loop : -1.92 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 513 HIS 0.004 0.001 HIS A 198 PHE 0.009 0.001 PHE A 954 TYR 0.014 0.001 TYR A1094 ARG 0.005 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.031 Fit side-chains REVERT: A 169 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 918 LYS cc_start: 0.7896 (tttt) cc_final: 0.7611 (ttmm) REVERT: A 943 ARG cc_start: 0.7955 (tmm-80) cc_final: 0.7459 (ttp-170) REVERT: A 1056 TYR cc_start: 0.8409 (m-80) cc_final: 0.8028 (m-80) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 0.2129 time to fit residues: 31.1363 Evaluate side-chains 95 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.0020 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8546 Z= 0.153 Angle : 0.576 13.793 11570 Z= 0.299 Chirality : 0.044 0.156 1186 Planarity : 0.003 0.043 1528 Dihedral : 4.763 35.157 1158 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 2.25 % Allowed : 18.56 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.25), residues: 1025 helix: -0.10 (1.58), residues: 13 sheet: 0.41 (0.37), residues: 229 loop : -1.88 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 513 HIS 0.005 0.001 HIS A 234 PHE 0.013 0.001 PHE A 175 TYR 0.013 0.001 TYR A1094 ARG 0.007 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.111 Fit side-chains REVERT: A 240 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: A 918 LYS cc_start: 0.7883 (tttt) cc_final: 0.7592 (ttmm) REVERT: A 943 ARG cc_start: 0.7947 (tmm-80) cc_final: 0.7448 (ttp-170) REVERT: A 962 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6473 (pm20) REVERT: A 1056 TYR cc_start: 0.8368 (m-80) cc_final: 0.8019 (m-80) outliers start: 20 outliers final: 16 residues processed: 108 average time/residue: 0.2174 time to fit residues: 33.0318 Evaluate side-chains 101 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 0.0370 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.0370 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8546 Z= 0.261 Angle : 0.633 14.913 11570 Z= 0.329 Chirality : 0.046 0.160 1186 Planarity : 0.004 0.045 1528 Dihedral : 5.123 36.041 1158 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 2.47 % Allowed : 19.24 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.25), residues: 1025 helix: -0.17 (1.55), residues: 13 sheet: 0.22 (0.36), residues: 232 loop : -1.89 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 513 HIS 0.005 0.001 HIS A 766 PHE 0.017 0.002 PHE A1075 TYR 0.017 0.001 TYR A1094 ARG 0.007 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.999 Fit side-chains REVERT: A 240 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7536 (tp40) REVERT: A 918 LYS cc_start: 0.7905 (tttt) cc_final: 0.7628 (ttmm) REVERT: A 943 ARG cc_start: 0.7962 (tmm-80) cc_final: 0.7483 (ttp-170) REVERT: A 962 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6494 (pm20) outliers start: 22 outliers final: 19 residues processed: 103 average time/residue: 0.2139 time to fit residues: 31.8080 Evaluate side-chains 101 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.0000 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8546 Z= 0.141 Angle : 0.573 13.722 11570 Z= 0.298 Chirality : 0.044 0.156 1186 Planarity : 0.003 0.042 1528 Dihedral : 4.721 34.998 1158 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.25 % Allowed : 19.69 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.26), residues: 1025 helix: 0.22 (1.62), residues: 13 sheet: 0.45 (0.37), residues: 229 loop : -1.84 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 513 HIS 0.004 0.001 HIS A 444 PHE 0.009 0.001 PHE A 954 TYR 0.013 0.001 TYR A 591 ARG 0.006 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.173 Fit side-chains REVERT: A 190 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7136 (pm20) REVERT: A 240 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: A 918 LYS cc_start: 0.7895 (tttt) cc_final: 0.7634 (ttmm) REVERT: A 943 ARG cc_start: 0.7926 (tmm-80) cc_final: 0.7448 (ttp-170) REVERT: A 962 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6458 (pm20) outliers start: 20 outliers final: 16 residues processed: 105 average time/residue: 0.2101 time to fit residues: 32.1648 Evaluate side-chains 102 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8546 Z= 0.187 Angle : 0.599 14.276 11570 Z= 0.311 Chirality : 0.045 0.154 1186 Planarity : 0.003 0.043 1528 Dihedral : 4.810 36.102 1158 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 2.25 % Allowed : 19.57 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.25), residues: 1025 helix: 0.18 (1.60), residues: 13 sheet: 0.33 (0.37), residues: 232 loop : -1.82 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 513 HIS 0.004 0.001 HIS A 444 PHE 0.017 0.001 PHE A 175 TYR 0.015 0.001 TYR A1094 ARG 0.005 0.000 ARG A 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.975 Fit side-chains REVERT: A 190 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: A 240 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: A 918 LYS cc_start: 0.7884 (tttt) cc_final: 0.7623 (ttmm) REVERT: A 943 ARG cc_start: 0.7937 (tmm-80) cc_final: 0.7457 (ttp-170) REVERT: A 962 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6471 (pm20) outliers start: 20 outliers final: 17 residues processed: 102 average time/residue: 0.1888 time to fit residues: 27.6034 Evaluate side-chains 103 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127198 restraints weight = 11025.199| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.21 r_work: 0.3435 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8546 Z= 0.283 Angle : 0.652 15.190 11570 Z= 0.340 Chirality : 0.047 0.161 1186 Planarity : 0.004 0.046 1528 Dihedral : 5.182 36.683 1158 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 2.36 % Allowed : 19.35 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.25), residues: 1025 helix: -0.11 (1.54), residues: 13 sheet: 0.26 (0.36), residues: 232 loop : -1.86 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 513 HIS 0.005 0.001 HIS A 198 PHE 0.018 0.002 PHE A1075 TYR 0.018 0.002 TYR A1094 ARG 0.006 0.000 ARG A 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2085.63 seconds wall clock time: 37 minutes 36.36 seconds (2256.36 seconds total)