Starting phenix.real_space_refine on Fri Sep 11 02:16:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xe6_22144/09_2026/6xe6_22144.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xe6_22144/09_2026/6xe6_22144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xe6_22144/09_2026/6xe6_22144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xe6_22144/09_2026/6xe6_22144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xe6_22144/09_2026/6xe6_22144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xe6_22144/09_2026/6xe6_22144.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xe6_22144/09_2026/6xe6_22144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xe6_22144/09_2026/6xe6_22144.cif" } resolution = 4.53 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= 0.000 sd= 0.003 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 54 5.16 5 C 4298 2.51 5 N 1022 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6530 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6340 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 36, 'TRANS': 789} Chain breaks: 10 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 3, 'PHE:plan': 4, 'TRP:plan': 3, 'ASP:plan': 5, 'HIS:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Unusual residues: {'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.52, per 1000 atoms: 0.23 Number of scatterers: 6530 At special positions: 0 Unit cell: (99.96, 74.97, 119.119, 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 54 16.00 O 1156 8.00 N 1022 7.00 C 4298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 367 " 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: 0.38 Conformation dependent library (CDL) restraints added in 307.6 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 62.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.547A pdb=" N TRP A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.534A pdb=" N ASN A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.701A pdb=" N CYS A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 432 removed outlier: 3.974A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 491 through 523 removed outlier: 4.545A pdb=" N GLN A 497 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N MET A 502 " --> pdb=" O ASP A 498 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 3.527A pdb=" N LYS A 523 " --> pdb=" O CYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 removed outlier: 3.562A pdb=" N THR A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.792A pdb=" N THR A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 563 " --> pdb=" O ASN A 559 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 569 " --> pdb=" O ILE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 588 removed outlier: 3.713A pdb=" N PHE A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 579 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 623 removed outlier: 3.617A pdb=" N THR A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 661 removed outlier: 3.827A pdb=" N ARG A 631 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 689 through 716 Proline residue: A 711 - end of helix Processing helix chain 'A' and resid 719 through 736 removed outlier: 3.874A pdb=" N PHE A 723 " --> pdb=" O TYR A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.659A pdb=" N ARG A 763 " --> pdb=" O HIS A 759 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP A 765 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 837 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.613A pdb=" N PHE A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 938 through 955 removed outlier: 3.558A pdb=" N GLN A 942 " --> pdb=" O GLU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1003 removed outlier: 3.507A pdb=" N ASP A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1030 removed outlier: 3.569A pdb=" N GLY A1025 " --> pdb=" O PHE A1021 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A1028 " --> pdb=" O VAL A1024 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A1030 " --> pdb=" O SER A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1062 removed outlier: 3.987A pdb=" N HIS A1055 " --> pdb=" O ASP A1051 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1059 " --> pdb=" O HIS A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1096 removed outlier: 4.625A pdb=" N MET A1085 " --> pdb=" O SER A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1134 removed outlier: 3.690A pdb=" N THR A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A1121 " --> pdb=" O CYS A1117 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS A1133 " --> pdb=" O CYS A1129 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1071 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: 0.97 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1050 1.33 - 1.45: 1802 1.45 - 1.57: 3758 1.57 - 1.70: 3 1.70 - 1.82: 85 Bond restraints: 6698 Sorted by residual: bond pdb=" CAX Y01 A1303 " pdb=" OAH Y01 A1303 " ideal model delta sigma weight residual 1.248 1.345 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" CAX Y01 A1304 " pdb=" OAH Y01 A1304 " ideal model delta sigma weight residual 1.248 1.344 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CAX Y01 A1302 " pdb=" OAH Y01 A1302 " ideal model delta sigma weight residual 1.248 1.344 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CAX Y01 A1305 " pdb=" OAH Y01 A1305 " ideal model delta sigma weight residual 1.248 1.344 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" CAX Y01 A1301 " pdb=" OAH Y01 A1301 " ideal model delta sigma weight residual 1.248 1.343 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 6693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 8057 2.13 - 4.26: 989 4.26 - 6.39: 74 6.39 - 8.52: 14 8.52 - 10.65: 4 Bond angle restraints: 9138 Sorted by residual: angle pdb=" C HIS A 759 " pdb=" N PRO A 760 " pdb=" CA PRO A 760 " ideal model delta sigma weight residual 119.84 130.49 -10.65 1.25e+00 6.40e-01 7.26e+01 angle pdb=" N PRO A 439 " pdb=" CA PRO A 439 " pdb=" CB PRO A 439 " ideal model delta sigma weight residual 103.25 111.16 -7.91 1.05e+00 9.07e-01 5.67e+01 angle pdb=" N PRO A 447 " pdb=" CA PRO A 447 " pdb=" CB PRO A 447 " ideal model delta sigma weight residual 103.00 110.09 -7.09 1.10e+00 8.26e-01 4.16e+01 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 103.00 109.71 -6.71 1.10e+00 8.26e-01 3.72e+01 angle pdb=" N TYR A 300 " pdb=" CA TYR A 300 " pdb=" C TYR A 300 " ideal model delta sigma weight residual 111.03 117.61 -6.58 1.11e+00 8.12e-01 3.52e+01 ... (remaining 9133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3432 17.13 - 34.26: 321 34.26 - 51.40: 95 51.40 - 68.53: 12 68.53 - 85.66: 2 Dihedral angle restraints: 3862 sinusoidal: 1439 harmonic: 2423 Sorted by residual: dihedral pdb=" CA LYS A 588 " pdb=" C LYS A 588 " pdb=" N PRO A 589 " pdb=" CA PRO A 589 " ideal model delta harmonic sigma weight residual -180.00 -150.51 -29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CB CYS A 323 " pdb=" SG CYS A 323 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 45.42 47.58 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CA ALA A1082 " pdb=" C ALA A1082 " pdb=" N MET A1083 " pdb=" CA MET A1083 " ideal model delta harmonic sigma weight residual -180.00 -153.97 -26.03 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 3859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 852 0.078 - 0.157: 179 0.157 - 0.235: 33 0.235 - 0.313: 7 0.313 - 0.392: 5 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CBG Y01 A1303 " pdb=" CAQ Y01 A1303 " pdb=" CBD Y01 A1303 " pdb=" CBI Y01 A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CBG Y01 A1305 " pdb=" CAQ Y01 A1305 " pdb=" CBD Y01 A1305 " pdb=" CBI Y01 A1305 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CBG Y01 A1304 " pdb=" CAQ Y01 A1304 " pdb=" CBD Y01 A1304 " pdb=" CBI Y01 A1304 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 1073 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 879 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 880 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 880 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 880 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 876 " 0.022 2.00e-02 2.50e+03 1.94e-02 5.64e+00 pdb=" CG HIS A 876 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS A 876 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 876 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 876 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 HIS A 876 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 316 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 317 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.032 5.00e-02 4.00e+02 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 3 1.86 - 2.62: 42 2.62 - 3.38: 9038 3.38 - 4.14: 14438 4.14 - 4.90: 24894 Nonbonded interactions: 48415 Sorted by model distance: nonbonded pdb=" OD1 ASN A 836 " pdb=" O1 NAG A1306 " model vdw 1.098 3.040 nonbonded pdb=" O SER A 820 " pdb=" NE2 GLN A 883 " model vdw 1.733 3.120 nonbonded pdb=" O PRO A 910 " pdb=" O ALA A 922 " model vdw 1.773 3.040 nonbonded pdb=" CG ASN A 836 " pdb=" O1 NAG A1306 " model vdw 2.181 3.270 nonbonded pdb=" O VAL A 610 " pdb=" OG1 THR A 614 " model vdw 2.266 3.040 ... (remaining 48410 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.520 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.830 Find NCS groups from input model: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.011 0.139 6699 Z= 0.739 Angle : 1.399 10.649 9140 Z= 0.913 Chirality : 0.072 0.392 1076 Planarity : 0.005 0.065 1104 Dihedral : 14.934 85.659 2283 Min Nonbonded Distance : 1.098 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 1.24 % Allowed : 11.32 % Favored : 87.44 % Rotamer: Outliers : 1.05 % Allowed : 10.38 % Favored : 88.57 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.22), residues: 804 helix: -2.36 (0.18), residues: 473 sheet: None (None), residues: 0 loop : -4.80 (0.25), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1078 TYR 0.019 0.002 TYR A 764 PHE 0.024 0.003 PHE A 839 TRP 0.019 0.002 TRP A 826 HIS 0.017 0.002 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.01083 / 0.74 ( 6698) covalent geometry : angle 1.39858 / 0.91 ( 9138) SS BOND : bond 0.00764 / 0.40 ( 1) SS BOND : angle 1.43864 / 0.80 ( 2) hydrogen bonds : bond 0.19759 / 13.41 ( 357) hydrogen bonds : angle 8.13855 / 5.84 ( 1071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 232 time to evaluate : 0.249 Fit side-chains REVERT: A 220 LEU cc_start: 0.9011 (pp) cc_final: 0.8792 (pp) REVERT: A 221 LEU cc_start: 0.9445 (tp) cc_final: 0.9056 (tp) REVERT: A 383 ARG cc_start: 0.7858 (mtt180) cc_final: 0.6452 (tpt-90) REVERT: A 433 ASP cc_start: 0.7710 (m-30) cc_final: 0.7435 (m-30) REVERT: A 453 MET cc_start: 0.5448 (pmm) cc_final: 0.4694 (pmm) REVERT: A 465 MET cc_start: 0.8420 (ttt) cc_final: 0.7960 (tpt) REVERT: A 573 ASP cc_start: 0.8357 (m-30) cc_final: 0.7791 (m-30) REVERT: A 578 CYS cc_start: 0.8937 (m) cc_final: 0.8594 (m) REVERT: A 581 TRP cc_start: 0.8950 (t-100) cc_final: 0.8185 (t-100) REVERT: A 597 VAL cc_start: 0.9693 (p) cc_final: 0.9402 (p) REVERT: A 620 TYR cc_start: 0.8790 (m-80) cc_final: 0.8145 (m-80) REVERT: A 796 GLU cc_start: 0.8965 (tt0) cc_final: 0.8687 (tt0) REVERT: A 798 ASN cc_start: 0.7981 (p0) cc_final: 0.7289 (t0) REVERT: A 970 ASN cc_start: 0.8277 (p0) cc_final: 0.8018 (p0) REVERT: A 1011 TYR cc_start: 0.8822 (m-10) cc_final: 0.6857 (m-80) REVERT: A 1029 LEU cc_start: 0.9265 (tp) cc_final: 0.9003 (tp) REVERT: A 1032 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.6775 (t60) REVERT: A 1034 LEU cc_start: 0.9423 (tt) cc_final: 0.8887 (mp) REVERT: A 1052 PHE cc_start: 0.8248 (m-80) cc_final: 0.8013 (m-80) REVERT: A 1083 MET cc_start: 0.8866 (mmp) cc_final: 0.8646 (mmm) REVERT: A 1101 THR cc_start: 0.9146 (m) cc_final: 0.8946 (m) REVERT: A 1112 MET cc_start: 0.8317 (ppp) cc_final: 0.7542 (ppp) outliers start: 7 outliers final: 2 residues processed: 236 average time/residue: 0.0542 time to fit residues: 18.1701 Evaluate side-chains 188 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 363 ASN A 559 ASN A 941 HIS A1128 GLN A1137 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113730 restraints weight = 14037.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117058 restraints weight = 8760.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119708 restraints weight = 6140.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121594 restraints weight = 4513.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122889 restraints weight = 3517.753| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6699 Z= 0.182 Angle : 0.772 8.694 9140 Z= 0.399 Chirality : 0.045 0.219 1076 Planarity : 0.005 0.039 1104 Dihedral : 7.994 57.203 934 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.70 % Favored : 89.80 % Rotamer: Outliers : 0.15 % Allowed : 3.61 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.91 (0.27), residues: 804 helix: -0.51 (0.22), residues: 485 sheet: None (None), residues: 0 loop : -4.34 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.035 0.002 TYR A1011 PHE 0.030 0.002 PHE A 725 TRP 0.026 0.002 TRP A 826 HIS 0.005 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6698) covalent geometry : angle 0.77187 / 0.40 ( 9138) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 1.36748 / 0.72 ( 2) hydrogen bonds : bond 0.05720 / 3.77 ( 357) hydrogen bonds : angle 5.11905 / 3.69 ( 1071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9318 (tp) cc_final: 0.8917 (tp) REVERT: A 302 ARG cc_start: 0.7194 (ptt-90) cc_final: 0.6953 (ptt-90) REVERT: A 383 ARG cc_start: 0.7816 (mtt180) cc_final: 0.6562 (tpt-90) REVERT: A 453 MET cc_start: 0.4865 (pmm) cc_final: 0.4656 (pmm) REVERT: A 465 MET cc_start: 0.8253 (ttt) cc_final: 0.7922 (tpp) REVERT: A 540 ILE cc_start: 0.9324 (pt) cc_final: 0.9086 (tp) REVERT: A 573 ASP cc_start: 0.8642 (m-30) cc_final: 0.8173 (m-30) REVERT: A 578 CYS cc_start: 0.9275 (m) cc_final: 0.8945 (m) REVERT: A 581 TRP cc_start: 0.8913 (t-100) cc_final: 0.7970 (t-100) REVERT: A 596 THR cc_start: 0.9344 (p) cc_final: 0.9090 (p) REVERT: A 597 VAL cc_start: 0.9729 (p) cc_final: 0.9371 (p) REVERT: A 636 TYR cc_start: 0.8760 (t80) cc_final: 0.8533 (t80) REVERT: A 645 TYR cc_start: 0.9466 (t80) cc_final: 0.9247 (t80) REVERT: A 659 HIS cc_start: 0.8857 (t70) cc_final: 0.8649 (t-170) REVERT: A 725 PHE cc_start: 0.8445 (t80) cc_final: 0.8056 (t80) REVERT: A 738 ILE cc_start: 0.7218 (mt) cc_final: 0.6996 (mt) REVERT: A 765 ASP cc_start: 0.7093 (m-30) cc_final: 0.6866 (m-30) REVERT: A 796 GLU cc_start: 0.8850 (tt0) cc_final: 0.8046 (tm-30) REVERT: A 798 ASN cc_start: 0.7875 (p0) cc_final: 0.7009 (t0) REVERT: A 927 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8892 (m-10) REVERT: A 1043 SER cc_start: 0.9387 (m) cc_final: 0.9012 (t) REVERT: A 1101 THR cc_start: 0.9133 (m) cc_final: 0.8923 (m) REVERT: A 1112 MET cc_start: 0.8378 (ppp) cc_final: 0.7938 (ppp) REVERT: A 1113 MET cc_start: 0.8637 (ttp) cc_final: 0.7690 (ttp) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.0506 time to fit residues: 15.5884 Evaluate side-chains 168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 58 optimal weight: 0.0020 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 644 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116948 restraints weight = 13850.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120678 restraints weight = 8394.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123344 restraints weight = 5661.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125272 restraints weight = 4113.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126583 restraints weight = 3182.379| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6699 Z= 0.151 Angle : 0.712 10.671 9140 Z= 0.363 Chirality : 0.043 0.186 1076 Planarity : 0.004 0.038 1104 Dihedral : 7.748 57.791 934 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.07 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.29), residues: 804 helix: 0.10 (0.23), residues: 483 sheet: None (None), residues: 0 loop : -3.90 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 233 TYR 0.015 0.002 TYR A1011 PHE 0.023 0.002 PHE A 839 TRP 0.022 0.002 TRP A 826 HIS 0.008 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 6698) covalent geometry : angle 0.71166 / 0.36 ( 9138) SS BOND : bond 0.00235 / 0.12 ( 1) SS BOND : angle 1.23245 / 0.65 ( 2) hydrogen bonds : bond 0.05238 / 3.48 ( 357) hydrogen bonds : angle 4.80115 / 3.47 ( 1071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LEU cc_start: 0.8758 (pp) cc_final: 0.8436 (pp) REVERT: A 221 LEU cc_start: 0.9336 (tp) cc_final: 0.8889 (tp) REVERT: A 233 ARG cc_start: 0.8867 (mtt180) cc_final: 0.8100 (mtt-85) REVERT: A 383 ARG cc_start: 0.7873 (mtt180) cc_final: 0.6592 (tpt-90) REVERT: A 453 MET cc_start: 0.4589 (pmm) cc_final: 0.3463 (pmm) REVERT: A 465 MET cc_start: 0.8310 (ttt) cc_final: 0.7856 (tmm) REVERT: A 536 ILE cc_start: 0.9123 (mm) cc_final: 0.8834 (mm) REVERT: A 573 ASP cc_start: 0.8727 (m-30) cc_final: 0.8519 (m-30) REVERT: A 578 CYS cc_start: 0.9311 (m) cc_final: 0.9049 (m) REVERT: A 581 TRP cc_start: 0.8847 (t-100) cc_final: 0.7840 (t-100) REVERT: A 596 THR cc_start: 0.9369 (p) cc_final: 0.9037 (p) REVERT: A 597 VAL cc_start: 0.9707 (p) cc_final: 0.9453 (p) REVERT: A 636 TYR cc_start: 0.8670 (t80) cc_final: 0.8422 (t80) REVERT: A 645 TYR cc_start: 0.9355 (t80) cc_final: 0.9065 (t80) REVERT: A 725 PHE cc_start: 0.8269 (t80) cc_final: 0.7746 (t80) REVERT: A 765 ASP cc_start: 0.7151 (m-30) cc_final: 0.6805 (m-30) REVERT: A 781 GLU cc_start: 0.8270 (tt0) cc_final: 0.7728 (tp30) REVERT: A 791 TRP cc_start: 0.8631 (m-10) cc_final: 0.8141 (m-10) REVERT: A 796 GLU cc_start: 0.8904 (tt0) cc_final: 0.7934 (tm-30) REVERT: A 798 ASN cc_start: 0.7803 (p0) cc_final: 0.7036 (t0) REVERT: A 1032 TRP cc_start: 0.8510 (t60) cc_final: 0.8053 (t-100) REVERT: A 1043 SER cc_start: 0.9253 (m) cc_final: 0.8862 (t) REVERT: A 1083 MET cc_start: 0.9013 (mmp) cc_final: 0.8449 (mmp) REVERT: A 1112 MET cc_start: 0.8538 (ppp) cc_final: 0.8112 (ppp) REVERT: A 1113 MET cc_start: 0.8694 (ttp) cc_final: 0.7764 (ttp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0491 time to fit residues: 14.9148 Evaluate side-chains 171 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 590 HIS A 837 GLN ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119795 restraints weight = 14188.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123097 restraints weight = 9019.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125352 restraints weight = 6281.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127102 restraints weight = 4701.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128375 restraints weight = 3732.707| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6699 Z= 0.139 Angle : 0.689 8.731 9140 Z= 0.354 Chirality : 0.042 0.184 1076 Planarity : 0.004 0.040 1104 Dihedral : 7.543 59.665 934 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.33 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.06 (0.29), residues: 804 helix: 0.24 (0.23), residues: 486 sheet: -5.29 (0.54), residues: 16 loop : -3.99 (0.30), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 547 TYR 0.039 0.002 TYR A1011 PHE 0.019 0.002 PHE A 554 TRP 0.020 0.001 TRP A 826 HIS 0.011 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 6698) covalent geometry : angle 0.68909 / 0.35 ( 9138) SS BOND : bond 0.00280 / 0.15 ( 1) SS BOND : angle 1.09467 / 0.59 ( 2) hydrogen bonds : bond 0.04972 / 3.29 ( 357) hydrogen bonds : angle 4.65143 / 3.37 ( 1071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9339 (tp) cc_final: 0.9069 (tp) REVERT: A 233 ARG cc_start: 0.8939 (mtt180) cc_final: 0.8724 (mtt-85) REVERT: A 302 ARG cc_start: 0.7325 (ptt-90) cc_final: 0.7098 (ptt-90) REVERT: A 383 ARG cc_start: 0.7831 (mtt180) cc_final: 0.6577 (tpt-90) REVERT: A 453 MET cc_start: 0.4782 (pmm) cc_final: 0.3643 (pmm) REVERT: A 465 MET cc_start: 0.8365 (ttt) cc_final: 0.7826 (tmm) REVERT: A 536 ILE cc_start: 0.9019 (mm) cc_final: 0.8684 (mm) REVERT: A 557 PHE cc_start: 0.9199 (p90) cc_final: 0.8969 (p90) REVERT: A 578 CYS cc_start: 0.9245 (m) cc_final: 0.8911 (m) REVERT: A 581 TRP cc_start: 0.8790 (t-100) cc_final: 0.8516 (t-100) REVERT: A 608 MET cc_start: 0.8913 (mtt) cc_final: 0.8639 (mtt) REVERT: A 645 TYR cc_start: 0.9369 (t80) cc_final: 0.8961 (t80) REVERT: A 725 PHE cc_start: 0.8359 (t80) cc_final: 0.7814 (t80) REVERT: A 765 ASP cc_start: 0.6900 (m-30) cc_final: 0.6663 (m-30) REVERT: A 781 GLU cc_start: 0.8211 (tt0) cc_final: 0.7770 (tp30) REVERT: A 796 GLU cc_start: 0.8721 (tt0) cc_final: 0.7887 (tm-30) REVERT: A 798 ASN cc_start: 0.7627 (p0) cc_final: 0.6799 (t0) REVERT: A 858 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9124 (mm-40) REVERT: A 970 ASN cc_start: 0.8265 (p0) cc_final: 0.8011 (p0) REVERT: A 990 LEU cc_start: 0.8872 (tt) cc_final: 0.8643 (tp) REVERT: A 1032 TRP cc_start: 0.8552 (t60) cc_final: 0.7665 (t60) REVERT: A 1033 GLU cc_start: 0.9115 (pm20) cc_final: 0.8844 (pm20) REVERT: A 1083 MET cc_start: 0.9087 (mmp) cc_final: 0.8873 (mmm) REVERT: A 1090 THR cc_start: 0.9287 (m) cc_final: 0.8980 (m) REVERT: A 1112 MET cc_start: 0.8507 (ppp) cc_final: 0.7735 (ppp) REVERT: A 1113 MET cc_start: 0.8626 (ttp) cc_final: 0.7655 (ttp) REVERT: A 1116 MET cc_start: 0.9405 (mmt) cc_final: 0.9169 (mmt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.0526 time to fit residues: 15.5302 Evaluate side-chains 171 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 977 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 = 0.3800 r_free = 0.3800 target = 0.144397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122934 restraints weight = 14125.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126300 restraints weight = 8907.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128692 restraints weight = 6174.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130411 restraints weight = 4584.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131664 restraints weight = 3608.222| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6699 Z= 0.138 Angle : 0.686 7.985 9140 Z= 0.349 Chirality : 0.042 0.172 1076 Planarity : 0.004 0.044 1104 Dihedral : 7.398 58.555 934 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.83 % Favored : 89.68 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.89 (0.29), residues: 804 helix: 0.37 (0.23), residues: 489 sheet: -4.98 (0.64), residues: 16 loop : -3.96 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1132 TYR 0.043 0.002 TYR A1011 PHE 0.018 0.002 PHE A 839 TRP 0.016 0.001 TRP A 826 HIS 0.012 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 6698) covalent geometry : angle 0.68578 / 0.35 ( 9138) SS BOND : bond 0.00260 / 0.14 ( 1) SS BOND : angle 1.03762 / 0.55 ( 2) hydrogen bonds : bond 0.04757 / 3.17 ( 357) hydrogen bonds : angle 4.58518 / 3.34 ( 1071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LEU cc_start: 0.8755 (pp) cc_final: 0.8398 (pp) REVERT: A 221 LEU cc_start: 0.9283 (tp) cc_final: 0.8780 (tp) REVERT: A 383 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6479 (tpt-90) REVERT: A 453 MET cc_start: 0.4736 (pmm) cc_final: 0.3643 (pmm) REVERT: A 465 MET cc_start: 0.8244 (ttt) cc_final: 0.7785 (tmm) REVERT: A 518 MET cc_start: 0.8626 (ttm) cc_final: 0.8127 (tpp) REVERT: A 530 MET cc_start: 0.9051 (tpt) cc_final: 0.8191 (tpt) REVERT: A 536 ILE cc_start: 0.8890 (mm) cc_final: 0.8526 (mm) REVERT: A 578 CYS cc_start: 0.9219 (m) cc_final: 0.8925 (m) REVERT: A 581 TRP cc_start: 0.8768 (t-100) cc_final: 0.7736 (t-100) REVERT: A 596 THR cc_start: 0.9352 (p) cc_final: 0.9019 (p) REVERT: A 597 VAL cc_start: 0.9640 (p) cc_final: 0.9383 (p) REVERT: A 645 TYR cc_start: 0.9356 (t80) cc_final: 0.9124 (t80) REVERT: A 710 LEU cc_start: 0.9469 (tt) cc_final: 0.9265 (tt) REVERT: A 725 PHE cc_start: 0.8080 (t80) cc_final: 0.7830 (t80) REVERT: A 765 ASP cc_start: 0.6824 (m-30) cc_final: 0.6521 (m-30) REVERT: A 781 GLU cc_start: 0.8205 (tt0) cc_final: 0.7737 (tp30) REVERT: A 791 TRP cc_start: 0.7443 (m-10) cc_final: 0.7087 (m-10) REVERT: A 796 GLU cc_start: 0.8737 (tt0) cc_final: 0.7911 (tm-30) REVERT: A 798 ASN cc_start: 0.7585 (p0) cc_final: 0.6753 (t0) REVERT: A 974 TYR cc_start: 0.8405 (t80) cc_final: 0.8149 (t80) REVERT: A 1032 TRP cc_start: 0.8445 (t60) cc_final: 0.7804 (t60) REVERT: A 1033 GLU cc_start: 0.9114 (pm20) cc_final: 0.8897 (pm20) REVERT: A 1083 MET cc_start: 0.8983 (mmp) cc_final: 0.8489 (mmp) REVERT: A 1112 MET cc_start: 0.8336 (ppp) cc_final: 0.7871 (ppp) REVERT: A 1113 MET cc_start: 0.8622 (ttp) cc_final: 0.7730 (ttp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0533 time to fit residues: 16.2896 Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN ** A 977 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 = 0.3828 r_free = 0.3828 target = 0.147167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123655 restraints weight = 14207.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127375 restraints weight = 8925.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129913 restraints weight = 6123.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131903 restraints weight = 4557.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133271 restraints weight = 3547.102| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6699 Z= 0.135 Angle : 0.682 8.188 9140 Z= 0.350 Chirality : 0.042 0.166 1076 Planarity : 0.004 0.046 1104 Dihedral : 7.309 58.000 934 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.33 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.74 (0.29), residues: 804 helix: 0.44 (0.23), residues: 485 sheet: -4.83 (0.77), residues: 16 loop : -3.75 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.055 0.002 TYR A1011 PHE 0.019 0.002 PHE A 557 TRP 0.018 0.001 TRP A 826 HIS 0.011 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 6698) covalent geometry : angle 0.68183 / 0.35 ( 9138) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 1.00606 / 0.54 ( 2) hydrogen bonds : bond 0.04721 / 3.16 ( 357) hydrogen bonds : angle 4.58639 / 3.33 ( 1071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9314 (tp) cc_final: 0.8950 (tp) REVERT: A 228 THR cc_start: 0.8879 (p) cc_final: 0.8410 (p) REVERT: A 383 ARG cc_start: 0.7818 (mtt180) cc_final: 0.6549 (tpp-160) REVERT: A 453 MET cc_start: 0.4637 (pmm) cc_final: 0.3557 (pmm) REVERT: A 465 MET cc_start: 0.8500 (ttt) cc_final: 0.7664 (tmm) REVERT: A 518 MET cc_start: 0.8601 (ttm) cc_final: 0.8070 (tpp) REVERT: A 557 PHE cc_start: 0.9241 (p90) cc_final: 0.9016 (p90) REVERT: A 578 CYS cc_start: 0.9202 (m) cc_final: 0.8884 (m) REVERT: A 581 TRP cc_start: 0.8754 (t-100) cc_final: 0.8502 (t-100) REVERT: A 584 THR cc_start: 0.9559 (p) cc_final: 0.9226 (p) REVERT: A 587 ASP cc_start: 0.8840 (p0) cc_final: 0.8171 (m-30) REVERT: A 645 TYR cc_start: 0.9339 (t80) cc_final: 0.9057 (t80) REVERT: A 725 PHE cc_start: 0.8193 (t80) cc_final: 0.7785 (t80) REVERT: A 742 MET cc_start: 0.6303 (tmm) cc_final: 0.6030 (tmm) REVERT: A 765 ASP cc_start: 0.6768 (m-30) cc_final: 0.6387 (m-30) REVERT: A 791 TRP cc_start: 0.7540 (m-10) cc_final: 0.7175 (m-10) REVERT: A 796 GLU cc_start: 0.8711 (tt0) cc_final: 0.7846 (tm-30) REVERT: A 798 ASN cc_start: 0.7572 (p0) cc_final: 0.6813 (t0) REVERT: A 811 THR cc_start: 0.8003 (p) cc_final: 0.7677 (p) REVERT: A 971 LEU cc_start: 0.9284 (pt) cc_final: 0.9007 (mt) REVERT: A 1083 MET cc_start: 0.9010 (mmp) cc_final: 0.8103 (mmm) REVERT: A 1112 MET cc_start: 0.8267 (ppp) cc_final: 0.7952 (ppp) REVERT: A 1113 MET cc_start: 0.8560 (ttp) cc_final: 0.7725 (ttp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.0499 time to fit residues: 14.5943 Evaluate side-chains 167 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120020 restraints weight = 14272.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123639 restraints weight = 8857.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126204 restraints weight = 6073.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128116 restraints weight = 4496.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129434 restraints weight = 3518.647| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6699 Z= 0.149 Angle : 0.707 8.656 9140 Z= 0.361 Chirality : 0.043 0.182 1076 Planarity : 0.005 0.049 1104 Dihedral : 7.171 57.329 934 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.70 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.73 (0.29), residues: 804 helix: 0.45 (0.23), residues: 487 sheet: -5.11 (0.59), residues: 16 loop : -3.78 (0.30), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 302 TYR 0.034 0.002 TYR A1011 PHE 0.027 0.002 PHE A 554 TRP 0.020 0.001 TRP A 826 HIS 0.009 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 6698) covalent geometry : angle 0.70649 / 0.36 ( 9138) SS BOND : bond 0.00268 / 0.14 ( 1) SS BOND : angle 0.97299 / 0.53 ( 2) hydrogen bonds : bond 0.04813 / 3.20 ( 357) hydrogen bonds : angle 4.50589 / 3.27 ( 1071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 220 LEU cc_start: 0.8800 (pp) cc_final: 0.8596 (pp) REVERT: A 221 LEU cc_start: 0.9335 (tp) cc_final: 0.8959 (tp) REVERT: A 383 ARG cc_start: 0.7892 (mtt180) cc_final: 0.6643 (tpp-160) REVERT: A 453 MET cc_start: 0.4910 (pmm) cc_final: 0.3707 (pmm) REVERT: A 465 MET cc_start: 0.8542 (ttt) cc_final: 0.7734 (tmm) REVERT: A 530 MET cc_start: 0.9467 (tpt) cc_final: 0.9233 (tpp) REVERT: A 536 ILE cc_start: 0.8970 (mm) cc_final: 0.8662 (mm) REVERT: A 578 CYS cc_start: 0.9236 (m) cc_final: 0.8995 (m) REVERT: A 581 TRP cc_start: 0.8852 (t-100) cc_final: 0.8611 (t-100) REVERT: A 584 THR cc_start: 0.9574 (p) cc_final: 0.9270 (p) REVERT: A 587 ASP cc_start: 0.8805 (p0) cc_final: 0.8206 (m-30) REVERT: A 645 TYR cc_start: 0.9399 (t80) cc_final: 0.9114 (t80) REVERT: A 725 PHE cc_start: 0.8464 (t80) cc_final: 0.7766 (t80) REVERT: A 742 MET cc_start: 0.6340 (tmm) cc_final: 0.6080 (tmm) REVERT: A 765 ASP cc_start: 0.6777 (m-30) cc_final: 0.6349 (m-30) REVERT: A 781 GLU cc_start: 0.8259 (tt0) cc_final: 0.7892 (tp30) REVERT: A 791 TRP cc_start: 0.7815 (m-10) cc_final: 0.7345 (m-10) REVERT: A 796 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8275 (tm-30) REVERT: A 798 ASN cc_start: 0.7768 (p0) cc_final: 0.7040 (t0) REVERT: A 811 THR cc_start: 0.8171 (p) cc_final: 0.7960 (p) REVERT: A 888 LEU cc_start: 0.8177 (mp) cc_final: 0.7932 (tt) REVERT: A 1007 ILE cc_start: 0.8285 (tt) cc_final: 0.7631 (tp) REVERT: A 1083 MET cc_start: 0.9237 (mmp) cc_final: 0.8366 (mmm) REVERT: A 1112 MET cc_start: 0.8299 (ppp) cc_final: 0.8040 (ppp) REVERT: A 1113 MET cc_start: 0.8721 (ttp) cc_final: 0.7809 (ttp) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.0489 time to fit residues: 14.5080 Evaluate side-chains 163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN A 778 HIS A 858 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.142150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119988 restraints weight = 13699.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123676 restraints weight = 8415.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126332 restraints weight = 5729.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128181 restraints weight = 4191.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129608 restraints weight = 3256.151| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6699 Z= 0.150 Angle : 0.726 7.537 9140 Z= 0.369 Chirality : 0.044 0.172 1076 Planarity : 0.005 0.049 1104 Dihedral : 7.329 57.248 934 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.83 % Favored : 89.68 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.73 (0.29), residues: 804 helix: 0.48 (0.23), residues: 489 sheet: -4.88 (0.71), residues: 18 loop : -3.86 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 302 TYR 0.030 0.002 TYR A1011 PHE 0.024 0.002 PHE A 554 TRP 0.020 0.001 TRP A 826 HIS 0.011 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6698) covalent geometry : angle 0.72574 / 0.37 ( 9138) SS BOND : bond 0.00209 / 0.11 ( 1) SS BOND : angle 0.98732 / 0.53 ( 2) hydrogen bonds : bond 0.04858 / 3.25 ( 357) hydrogen bonds : angle 4.46006 / 3.25 ( 1071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9358 (tp) cc_final: 0.9007 (tp) REVERT: A 383 ARG cc_start: 0.7809 (mtt180) cc_final: 0.6628 (tpt170) REVERT: A 453 MET cc_start: 0.5145 (pmm) cc_final: 0.3934 (pmm) REVERT: A 465 MET cc_start: 0.8484 (ttt) cc_final: 0.7720 (tmm) REVERT: A 536 ILE cc_start: 0.9004 (mm) cc_final: 0.8651 (mm) REVERT: A 578 CYS cc_start: 0.9246 (m) cc_final: 0.8978 (m) REVERT: A 581 TRP cc_start: 0.8873 (t-100) cc_final: 0.8628 (t-100) REVERT: A 584 THR cc_start: 0.9554 (p) cc_final: 0.9232 (p) REVERT: A 587 ASP cc_start: 0.8672 (p0) cc_final: 0.8150 (m-30) REVERT: A 725 PHE cc_start: 0.8468 (t80) cc_final: 0.7943 (t80) REVERT: A 765 ASP cc_start: 0.6766 (m-30) cc_final: 0.6346 (m-30) REVERT: A 781 GLU cc_start: 0.8286 (tt0) cc_final: 0.7621 (tp30) REVERT: A 791 TRP cc_start: 0.7918 (m-10) cc_final: 0.7526 (m-10) REVERT: A 796 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8288 (tm-30) REVERT: A 798 ASN cc_start: 0.7740 (p0) cc_final: 0.7036 (t0) REVERT: A 888 LEU cc_start: 0.8229 (mp) cc_final: 0.7962 (tp) REVERT: A 1007 ILE cc_start: 0.8258 (tt) cc_final: 0.7510 (tp) REVERT: A 1083 MET cc_start: 0.8909 (mmp) cc_final: 0.8307 (ttm) REVERT: A 1097 MET cc_start: 0.8450 (tpp) cc_final: 0.8249 (tpp) REVERT: A 1112 MET cc_start: 0.8308 (ppp) cc_final: 0.8050 (ppp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0484 time to fit residues: 14.4489 Evaluate side-chains 161 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 356 ASN A 363 ASN A 837 GLN ** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123000 restraints weight = 13769.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126869 restraints weight = 8407.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129646 restraints weight = 5696.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131586 restraints weight = 4128.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133047 restraints weight = 3192.957| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6699 Z= 0.137 Angle : 0.719 8.883 9140 Z= 0.362 Chirality : 0.043 0.226 1076 Planarity : 0.004 0.048 1104 Dihedral : 7.171 57.519 934 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.07 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.67 (0.29), residues: 804 helix: 0.52 (0.23), residues: 491 sheet: -4.57 (0.90), residues: 18 loop : -3.86 (0.30), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 302 TYR 0.028 0.002 TYR A1011 PHE 0.022 0.002 PHE A 554 TRP 0.019 0.001 TRP A 826 HIS 0.012 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 6698) covalent geometry : angle 0.71900 / 0.36 ( 9138) SS BOND : bond 0.00195 / 0.10 ( 1) SS BOND : angle 1.00405 / 0.54 ( 2) hydrogen bonds : bond 0.04709 / 3.16 ( 357) hydrogen bonds : angle 4.36426 / 3.17 ( 1071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 220 LEU cc_start: 0.8833 (pp) cc_final: 0.8549 (pp) REVERT: A 221 LEU cc_start: 0.9290 (tp) cc_final: 0.8719 (tp) REVERT: A 383 ARG cc_start: 0.7800 (mtt180) cc_final: 0.6596 (tpp-160) REVERT: A 465 MET cc_start: 0.8470 (ttt) cc_final: 0.7780 (tmm) REVERT: A 518 MET cc_start: 0.8741 (ttm) cc_final: 0.8175 (tpp) REVERT: A 530 MET cc_start: 0.9430 (tpt) cc_final: 0.9102 (tpp) REVERT: A 536 ILE cc_start: 0.8910 (mm) cc_final: 0.8537 (mm) REVERT: A 577 LEU cc_start: 0.9139 (tp) cc_final: 0.8914 (tt) REVERT: A 584 THR cc_start: 0.9534 (p) cc_final: 0.9186 (p) REVERT: A 587 ASP cc_start: 0.8672 (p0) cc_final: 0.8221 (m-30) REVERT: A 725 PHE cc_start: 0.8523 (t80) cc_final: 0.7979 (t80) REVERT: A 765 ASP cc_start: 0.6818 (m-30) cc_final: 0.6351 (m-30) REVERT: A 781 GLU cc_start: 0.8270 (tt0) cc_final: 0.7750 (tm-30) REVERT: A 791 TRP cc_start: 0.7842 (m-10) cc_final: 0.7481 (m-10) REVERT: A 796 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8284 (tm-30) REVERT: A 798 ASN cc_start: 0.7712 (p0) cc_final: 0.6966 (t0) REVERT: A 811 THR cc_start: 0.8149 (p) cc_final: 0.7832 (p) REVERT: A 888 LEU cc_start: 0.8277 (mp) cc_final: 0.7999 (tp) REVERT: A 972 GLU cc_start: 0.8531 (tt0) cc_final: 0.8300 (tt0) REVERT: A 1007 ILE cc_start: 0.8178 (tt) cc_final: 0.7380 (tp) REVERT: A 1083 MET cc_start: 0.9072 (mmp) cc_final: 0.8340 (ttm) REVERT: A 1113 MET cc_start: 0.8684 (ttp) cc_final: 0.7785 (ttp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.0517 time to fit residues: 15.7324 Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 0.0070 chunk 46 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 324 ASN A 356 ASN A 363 ASN A 858 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124231 restraints weight = 13499.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127957 restraints weight = 8341.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130696 restraints weight = 5704.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132669 restraints weight = 4180.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134025 restraints weight = 3235.701| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6699 Z= 0.138 Angle : 0.733 10.801 9140 Z= 0.370 Chirality : 0.044 0.220 1076 Planarity : 0.005 0.049 1104 Dihedral : 7.092 57.176 934 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.32 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.71 (0.29), residues: 804 helix: 0.43 (0.23), residues: 494 sheet: -4.25 (1.04), residues: 18 loop : -3.85 (0.30), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 302 TYR 0.025 0.002 TYR A1011 PHE 0.021 0.002 PHE A 554 TRP 0.018 0.001 TRP A 826 HIS 0.013 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 6698) covalent geometry : angle 0.73297 / 0.37 ( 9138) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 1.66162 / 0.89 ( 2) hydrogen bonds : bond 0.04846 / 3.29 ( 357) hydrogen bonds : angle 4.46536 / 3.26 ( 1071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9279 (tp) cc_final: 0.8900 (tp) REVERT: A 383 ARG cc_start: 0.7775 (mtt180) cc_final: 0.6737 (tpt170) REVERT: A 453 MET cc_start: 0.4579 (pmm) cc_final: 0.3835 (pmm) REVERT: A 465 MET cc_start: 0.8435 (ttt) cc_final: 0.7791 (tmm) REVERT: A 518 MET cc_start: 0.8756 (ttm) cc_final: 0.8231 (tpp) REVERT: A 525 MET cc_start: 0.7411 (mtt) cc_final: 0.6873 (mmt) REVERT: A 536 ILE cc_start: 0.8841 (mm) cc_final: 0.8466 (mm) REVERT: A 573 ASP cc_start: 0.8098 (m-30) cc_final: 0.7845 (m-30) REVERT: A 577 LEU cc_start: 0.9132 (tp) cc_final: 0.8684 (tt) REVERT: A 584 THR cc_start: 0.9548 (p) cc_final: 0.9163 (p) REVERT: A 587 ASP cc_start: 0.8686 (p0) cc_final: 0.8234 (m-30) REVERT: A 645 TYR cc_start: 0.9415 (t80) cc_final: 0.9151 (t80) REVERT: A 742 MET cc_start: 0.6489 (tmm) cc_final: 0.6239 (tmm) REVERT: A 765 ASP cc_start: 0.6911 (m-30) cc_final: 0.6448 (m-30) REVERT: A 781 GLU cc_start: 0.8233 (tt0) cc_final: 0.7547 (tp30) REVERT: A 789 VAL cc_start: 0.8889 (m) cc_final: 0.8620 (m) REVERT: A 791 TRP cc_start: 0.7843 (m-10) cc_final: 0.7380 (m-10) REVERT: A 796 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8283 (tm-30) REVERT: A 798 ASN cc_start: 0.7646 (p0) cc_final: 0.6975 (t0) REVERT: A 811 THR cc_start: 0.8011 (p) cc_final: 0.7774 (p) REVERT: A 884 GLU cc_start: 0.6908 (mp0) cc_final: 0.6390 (tp30) REVERT: A 972 GLU cc_start: 0.8551 (tt0) cc_final: 0.8304 (tt0) REVERT: A 1007 ILE cc_start: 0.8132 (tt) cc_final: 0.7310 (tp) REVERT: A 1083 MET cc_start: 0.9084 (mmp) cc_final: 0.8263 (ttm) REVERT: A 1113 MET cc_start: 0.8647 (ttp) cc_final: 0.7788 (ttp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0509 time to fit residues: 15.1812 Evaluate side-chains 170 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.0570 chunk 48 optimal weight: 0.0870 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 356 ASN A 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126516 restraints weight = 13338.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130259 restraints weight = 8314.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133011 restraints weight = 5686.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135030 restraints weight = 4162.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136507 restraints weight = 3227.236| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6699 Z= 0.137 Angle : 0.719 9.955 9140 Z= 0.363 Chirality : 0.044 0.223 1076 Planarity : 0.004 0.051 1104 Dihedral : 6.923 56.549 934 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.20 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.56 (0.29), residues: 804 helix: 0.49 (0.23), residues: 489 sheet: -4.01 (1.12), residues: 18 loop : -3.60 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 302 TYR 0.021 0.002 TYR A1011 PHE 0.034 0.002 PHE A1126 TRP 0.016 0.001 TRP A 826 HIS 0.013 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 6698) covalent geometry : angle 0.71899 / 0.36 ( 9138) SS BOND : bond 0.00218 / 0.11 ( 1) SS BOND : angle 1.04357 / 0.55 ( 2) hydrogen bonds : bond 0.04723 / 3.22 ( 357) hydrogen bonds : angle 4.44487 / 3.25 ( 1071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1014.67 seconds wall clock time: 18 minutes 21.08 seconds (1101.08 seconds total)