Starting phenix.real_space_refine on Fri Aug 22 19:21:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qy7_18747/08_2025/8qy7_18747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qy7_18747/08_2025/8qy7_18747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qy7_18747/08_2025/8qy7_18747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qy7_18747/08_2025/8qy7_18747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qy7_18747/08_2025/8qy7_18747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qy7_18747/08_2025/8qy7_18747.map" } resolution = 2.66 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= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 4582 2.51 5 N 1241 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7167 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7167 Classifications: {'peptide': 893} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 50, 'TRANS': 842} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.41, per 1000 atoms: 0.20 Number of scatterers: 7167 At special positions: 0 Unit cell: (82.368, 118.144, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1329 8.00 N 1241 7.00 C 4582 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: 0.53 Conformation dependent library (CDL) restraints added in 352.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 9 sheets defined 50.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 147 through 165 Processing helix chain 'A' and resid 169 through 188 Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.613A pdb=" N LYS A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.845A pdb=" N ILE A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.238A pdb=" N PHE A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.808A pdb=" N VAL A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 360 through 377 removed outlier: 3.637A pdb=" N LEU A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'A' and resid 581 through 596 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 641 through 656 Processing helix chain 'A' and resid 657 through 661 removed outlier: 3.908A pdb=" N GLY A 660 " --> pdb=" O TYR A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 3.657A pdb=" N LYS A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.678A pdb=" N GLN A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 736 removed outlier: 3.589A pdb=" N LYS A 736 " --> pdb=" O GLN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 765 through 777 removed outlier: 4.286A pdb=" N LEU A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 844 through 864 Processing helix chain 'A' and resid 875 through 888 Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.121A pdb=" N VAL A 892 " --> pdb=" O HIS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.803A pdb=" N ARG A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP A 900 " --> pdb=" O PRO A 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 900' Processing helix chain 'A' and resid 902 through 919 Processing helix chain 'A' and resid 929 through 945 Processing helix chain 'A' and resid 959 through 975 Processing helix chain 'A' and resid 1008 through 1017 Processing helix chain 'A' and resid 1042 through 1059 Processing helix chain 'A' and resid 1069 through 1073 Processing helix chain 'A' and resid 1074 through 1079 removed outlier: 4.242A pdb=" N LYS A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1074 through 1079' Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104 removed outlier: 6.222A pdb=" N ARG A 98 " --> pdb=" O TRP A 119 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP A 119 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 100 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 117 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 113 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 133 removed outlier: 3.570A pdb=" N ILE A 136 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 201 removed outlier: 6.537A pdb=" N HIS A 199 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE A 261 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 201 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 214 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.567A pdb=" N ILE A 327 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE A 324 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 663 through 666 removed outlier: 6.442A pdb=" N LEU A 664 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN A 636 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 707 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 638 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 637 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP A 730 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 639 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 725 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LEU A 818 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 606 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 834 removed outlier: 6.540A pdb=" N ILE A 833 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A 998 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N TYR A1031 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A1000 " --> pdb=" O TYR A1031 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS A 922 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A 999 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL A 949 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 841 through 842 removed outlier: 5.963A pdb=" N LEU A 841 " --> pdb=" O ARG A1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 340 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.31: 1222 1.31 - 1.60: 6089 1.60 - 1.90: 21 1.90 - 2.20: 1 2.20 - 2.50: 1 Bond restraints: 7334 Sorted by residual: bond pdb=" CB PRO A 830 " pdb=" CG PRO A 830 " ideal model delta sigma weight residual 1.492 2.498 -1.006 5.00e-02 4.00e+02 4.05e+02 bond pdb=" CG PRO A 830 " pdb=" CD PRO A 830 " ideal model delta sigma weight residual 1.503 1.007 0.496 3.40e-02 8.65e+02 2.13e+02 bond pdb=" CB PRO A 794 " pdb=" CG PRO A 794 " ideal model delta sigma weight residual 1.492 2.086 -0.594 5.00e-02 4.00e+02 1.41e+02 bond pdb=" CG PRO A 723 " pdb=" CD PRO A 723 " ideal model delta sigma weight residual 1.503 1.115 0.388 3.40e-02 8.65e+02 1.30e+02 bond pdb=" CB PRO A 723 " pdb=" CG PRO A 723 " ideal model delta sigma weight residual 1.492 1.020 0.472 5.00e-02 4.00e+02 8.93e+01 ... (remaining 7329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.39: 9961 17.39 - 34.79: 8 34.79 - 52.18: 0 52.18 - 69.57: 1 69.57 - 86.97: 2 Bond angle restraints: 9972 Sorted by residual: angle pdb=" CB PRO A 830 " pdb=" CG PRO A 830 " pdb=" CD PRO A 830 " ideal model delta sigma weight residual 106.10 19.13 86.97 3.20e+00 9.77e-02 7.39e+02 angle pdb=" CA PRO A 794 " pdb=" N PRO A 794 " pdb=" CD PRO A 794 " ideal model delta sigma weight residual 112.00 78.00 34.00 1.40e+00 5.10e-01 5.90e+02 angle pdb=" CB PRO A 723 " pdb=" CG PRO A 723 " pdb=" CD PRO A 723 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CB PRO A 794 " pdb=" CG PRO A 794 " pdb=" CD PRO A 794 " ideal model delta sigma weight residual 106.10 39.67 66.43 3.20e+00 9.77e-02 4.31e+02 angle pdb=" CA PRO A 723 " pdb=" CB PRO A 723 " pdb=" CG PRO A 723 " ideal model delta sigma weight residual 104.50 70.40 34.10 1.90e+00 2.77e-01 3.22e+02 ... (remaining 9967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 4247 26.67 - 53.33: 148 53.33 - 80.00: 27 80.00 - 106.66: 5 106.66 - 133.33: 1 Dihedral angle restraints: 4428 sinusoidal: 1816 harmonic: 2612 Sorted by residual: dihedral pdb=" N PRO A 830 " pdb=" CG PRO A 830 " pdb=" CD PRO A 830 " pdb=" CB PRO A 830 " ideal model delta sinusoidal sigma weight residual -30.00 -163.33 133.33 1 1.50e+01 4.44e-03 7.19e+01 dihedral pdb=" N PRO A 794 " pdb=" CG PRO A 794 " pdb=" CD PRO A 794 " pdb=" CB PRO A 794 " ideal model delta sinusoidal sigma weight residual -30.00 -131.21 101.21 1 1.50e+01 4.44e-03 5.10e+01 dihedral pdb=" CA ILE A 336 " pdb=" C ILE A 336 " pdb=" N THR A 337 " pdb=" CA THR A 337 " ideal model delta harmonic sigma weight residual 180.00 149.20 30.80 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 4425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 732 0.037 - 0.074: 264 0.074 - 0.111: 89 0.111 - 0.148: 29 0.148 - 0.184: 3 Chirality restraints: 1117 Sorted by residual: chirality pdb=" CB THR A 167 " pdb=" CA THR A 167 " pdb=" OG1 THR A 167 " pdb=" CG2 THR A 167 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CG LEU A1051 " pdb=" CB LEU A1051 " pdb=" CD1 LEU A1051 " pdb=" CD2 LEU A1051 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE A 681 " pdb=" N ILE A 681 " pdb=" C ILE A 681 " pdb=" CB ILE A 681 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1114 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 793 " 0.101 5.00e-02 4.00e+02 1.29e-01 2.67e+01 pdb=" N PRO A 794 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 794 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 794 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 681 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 682 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 122 " -0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO A 123 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.053 5.00e-02 4.00e+02 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 25 2.41 - 3.03: 4293 3.03 - 3.66: 10874 3.66 - 4.28: 17076 4.28 - 4.90: 28338 Nonbonded interactions: 60606 Sorted by model distance: nonbonded pdb=" O TYR A 74 " pdb=" OE1 GLU A 78 " model vdw 1.791 3.040 nonbonded pdb=" O GLN A 410 " pdb=" OE1 GLU A 414 " model vdw 2.051 3.040 nonbonded pdb=" OD1 ASN A 331 " pdb=" N THR A 332 " model vdw 2.093 3.120 nonbonded pdb=" NZ LYS A 848 " pdb=" OE2 GLU A1039 " model vdw 2.208 3.120 nonbonded pdb=" O ASP A 609 " pdb=" NZ LYS A 615 " model vdw 2.211 3.120 ... (remaining 60601 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.860 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:5.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.018 1.006 7334 Z= 0.489 Angle : 1.706 86.966 9972 Z= 0.740 Chirality : 0.045 0.184 1117 Planarity : 0.010 0.129 1293 Dihedral : 14.575 133.327 2722 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.28), residues: 885 helix: 1.32 (0.24), residues: 395 sheet: -0.31 (0.43), residues: 119 loop : -0.22 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 98 TYR 0.014 0.001 TYR A 676 PHE 0.018 0.002 PHE A 773 TRP 0.045 0.002 TRP A 399 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.01795 ( 7334) covalent geometry : angle 1.70636 ( 9972) hydrogen bonds : bond 0.14021 ( 340) hydrogen bonds : angle 6.20178 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.243 Fit side-chains REVERT: A 342 ILE cc_start: 0.8255 (mm) cc_final: 0.7976 (mm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.5946 time to fit residues: 95.0914 Evaluate side-chains 109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 23 GLN A 25 GLN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN A 369 GLN A 400 HIS A 692 ASN A 857 ASN ** A 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 995 GLN A 998 ASN A 999 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128162 restraints weight = 7887.445| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.21 r_work: 0.3451 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7334 Z= 0.173 Angle : 0.623 11.729 9972 Z= 0.320 Chirality : 0.044 0.148 1117 Planarity : 0.008 0.092 1293 Dihedral : 4.674 31.574 954 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.21 % Allowed : 8.23 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.28), residues: 885 helix: 1.64 (0.25), residues: 400 sheet: -0.61 (0.44), residues: 119 loop : -0.23 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1036 TYR 0.015 0.001 TYR A 676 PHE 0.016 0.002 PHE A 626 TRP 0.015 0.002 TRP A 590 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7334) covalent geometry : angle 0.62270 ( 9972) hydrogen bonds : bond 0.04375 ( 340) hydrogen bonds : angle 4.87208 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.177 Fit side-chains REVERT: A 118 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: A 142 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6007 (tm-30) REVERT: A 242 LEU cc_start: 0.8316 (mp) cc_final: 0.7914 (tp) REVERT: A 342 ILE cc_start: 0.7899 (mm) cc_final: 0.7562 (mm) REVERT: A 586 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: A 649 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6111 (tm-30) REVERT: A 731 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7765 (mp0) REVERT: A 995 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: A 1059 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6834 (mtt90) outliers start: 25 outliers final: 8 residues processed: 125 average time/residue: 0.6504 time to fit residues: 84.7819 Evaluate side-chains 117 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 857 ASN A 973 GLN A 995 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127155 restraints weight = 7852.822| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.20 r_work: 0.3439 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7334 Z= 0.173 Angle : 0.569 6.186 9972 Z= 0.293 Chirality : 0.044 0.144 1117 Planarity : 0.007 0.058 1293 Dihedral : 4.613 30.380 954 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.11 % Allowed : 9.38 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.28), residues: 885 helix: 1.82 (0.25), residues: 393 sheet: -0.64 (0.44), residues: 119 loop : -0.13 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 65 TYR 0.014 0.001 TYR A 294 PHE 0.016 0.002 PHE A 626 TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS A 999 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 7334) covalent geometry : angle 0.56890 ( 9972) hydrogen bonds : bond 0.04274 ( 340) hydrogen bonds : angle 4.68229 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.266 Fit side-chains REVERT: A 118 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: A 142 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6065 (tm-30) REVERT: A 242 LEU cc_start: 0.8365 (mp) cc_final: 0.7952 (tp) REVERT: A 342 ILE cc_start: 0.8033 (mm) cc_final: 0.7634 (mm) REVERT: A 393 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7336 (mp-120) REVERT: A 586 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: A 649 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: A 731 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7784 (mp0) REVERT: A 971 ASP cc_start: 0.7593 (m-30) cc_final: 0.7339 (m-30) REVERT: A 995 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6914 (mp10) REVERT: A 1059 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6886 (mtt90) outliers start: 32 outliers final: 13 residues processed: 131 average time/residue: 0.6191 time to fit residues: 84.9607 Evaluate side-chains 127 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 857 ASN A 975 GLN A 995 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123273 restraints weight = 8011.052| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.23 r_work: 0.3396 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 7334 Z= 0.276 Angle : 0.633 6.303 9972 Z= 0.325 Chirality : 0.047 0.154 1117 Planarity : 0.007 0.055 1293 Dihedral : 4.892 29.584 954 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.50 % Allowed : 10.41 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.28), residues: 885 helix: 1.43 (0.25), residues: 394 sheet: -0.61 (0.47), residues: 109 loop : -0.30 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 249 TYR 0.018 0.002 TYR A 294 PHE 0.020 0.002 PHE A 626 TRP 0.020 0.002 TRP A 119 HIS 0.007 0.001 HIS A 999 Details of bonding type rmsd covalent geometry : bond 0.00672 ( 7334) covalent geometry : angle 0.63344 ( 9972) hydrogen bonds : bond 0.04854 ( 340) hydrogen bonds : angle 4.82672 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.273 Fit side-chains REVERT: A 118 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: A 142 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6024 (tm-30) REVERT: A 242 LEU cc_start: 0.8407 (mp) cc_final: 0.7971 (tp) REVERT: A 256 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6906 (mt-10) REVERT: A 342 ILE cc_start: 0.8176 (mm) cc_final: 0.7826 (mm) REVERT: A 586 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: A 649 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6300 (tm-30) REVERT: A 971 ASP cc_start: 0.7576 (m-30) cc_final: 0.7314 (m-30) REVERT: A 995 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6822 (mp10) REVERT: A 1059 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6882 (mtt90) outliers start: 35 outliers final: 18 residues processed: 128 average time/residue: 0.6300 time to fit residues: 84.5488 Evaluate side-chains 132 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 63 optimal weight: 0.4980 chunk 84 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 857 ASN A 975 GLN A 995 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.164374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127739 restraints weight = 7891.451| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.20 r_work: 0.3430 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7334 Z= 0.134 Angle : 0.519 5.196 9972 Z= 0.270 Chirality : 0.042 0.137 1117 Planarity : 0.006 0.054 1293 Dihedral : 4.545 29.625 954 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.47 % Allowed : 11.95 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.29), residues: 885 helix: 1.78 (0.25), residues: 393 sheet: -0.65 (0.44), residues: 124 loop : -0.05 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 249 TYR 0.014 0.001 TYR A 294 PHE 0.013 0.001 PHE A 626 TRP 0.018 0.001 TRP A 234 HIS 0.007 0.001 HIS A 999 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7334) covalent geometry : angle 0.51887 ( 9972) hydrogen bonds : bond 0.03915 ( 340) hydrogen bonds : angle 4.50470 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.241 Fit side-chains REVERT: A 142 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6000 (tm-30) REVERT: A 242 LEU cc_start: 0.8365 (mp) cc_final: 0.7956 (tp) REVERT: A 256 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6775 (mt-10) REVERT: A 316 ASP cc_start: 0.7786 (m-30) cc_final: 0.7355 (m-30) REVERT: A 342 ILE cc_start: 0.8005 (mm) cc_final: 0.7709 (mm) REVERT: A 586 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: A 971 ASP cc_start: 0.7449 (m-30) cc_final: 0.7168 (m-30) REVERT: A 995 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: A 1049 ASP cc_start: 0.7525 (m-30) cc_final: 0.7232 (m-30) REVERT: A 1059 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6817 (mtt90) outliers start: 27 outliers final: 14 residues processed: 133 average time/residue: 0.5482 time to fit residues: 76.8704 Evaluate side-chains 127 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 82 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN A 292 ASN A 857 ASN A 973 GLN A 975 GLN A 995 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126971 restraints weight = 7881.425| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.20 r_work: 0.3415 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7334 Z= 0.154 Angle : 0.529 5.220 9972 Z= 0.275 Chirality : 0.043 0.141 1117 Planarity : 0.006 0.053 1293 Dihedral : 4.506 28.690 954 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.11 % Allowed : 12.60 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.28), residues: 885 helix: 1.82 (0.25), residues: 393 sheet: -0.73 (0.45), residues: 119 loop : -0.10 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.015 0.001 TYR A 294 PHE 0.014 0.002 PHE A 626 TRP 0.016 0.001 TRP A 234 HIS 0.006 0.001 HIS A 999 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 7334) covalent geometry : angle 0.52911 ( 9972) hydrogen bonds : bond 0.04042 ( 340) hydrogen bonds : angle 4.47063 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.296 Fit side-chains REVERT: A 118 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: A 142 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6028 (tm-30) REVERT: A 242 LEU cc_start: 0.8386 (mp) cc_final: 0.8067 (tt) REVERT: A 256 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 316 ASP cc_start: 0.7859 (m-30) cc_final: 0.7623 (m-30) REVERT: A 342 ILE cc_start: 0.8109 (mm) cc_final: 0.7725 (mm) REVERT: A 393 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7469 (mp-120) REVERT: A 586 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: A 649 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6179 (tm-30) REVERT: A 966 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6496 (tp-100) REVERT: A 971 ASP cc_start: 0.7413 (m-30) cc_final: 0.7115 (m-30) REVERT: A 995 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6744 (mp10) REVERT: A 1049 ASP cc_start: 0.7606 (m-30) cc_final: 0.7355 (m-30) REVERT: A 1059 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6842 (mtt90) outliers start: 32 outliers final: 17 residues processed: 132 average time/residue: 0.5335 time to fit residues: 74.1278 Evaluate side-chains 134 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 0.0070 chunk 42 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN A 857 ASN A 975 GLN A 995 GLN A1008 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.167548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130998 restraints weight = 7843.083| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.18 r_work: 0.3486 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7334 Z= 0.116 Angle : 0.499 4.967 9972 Z= 0.260 Chirality : 0.042 0.136 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.363 28.354 954 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.08 % Allowed : 14.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.29), residues: 885 helix: 1.99 (0.26), residues: 396 sheet: -0.65 (0.45), residues: 124 loop : -0.02 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.014 0.001 TYR A 294 PHE 0.011 0.001 PHE A 626 TRP 0.017 0.001 TRP A 234 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7334) covalent geometry : angle 0.49852 ( 9972) hydrogen bonds : bond 0.03712 ( 340) hydrogen bonds : angle 4.34065 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.274 Fit side-chains REVERT: A 71 GLU cc_start: 0.7432 (pm20) cc_final: 0.7222 (pm20) REVERT: A 142 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6089 (tm-30) REVERT: A 242 LEU cc_start: 0.8373 (mp) cc_final: 0.8084 (tt) REVERT: A 312 GLN cc_start: 0.8121 (tp40) cc_final: 0.7857 (tp-100) REVERT: A 316 ASP cc_start: 0.7835 (m-30) cc_final: 0.7552 (m-30) REVERT: A 342 ILE cc_start: 0.7946 (mm) cc_final: 0.7659 (mm) REVERT: A 586 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: A 649 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6187 (tm-30) REVERT: A 966 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6638 (tp-100) REVERT: A 971 ASP cc_start: 0.7423 (m-30) cc_final: 0.7154 (m-30) REVERT: A 995 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6716 (mp10) REVERT: A 1049 ASP cc_start: 0.7648 (m-30) cc_final: 0.7380 (m-30) REVERT: A 1059 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6853 (mtt90) outliers start: 24 outliers final: 12 residues processed: 131 average time/residue: 0.5477 time to fit residues: 75.5399 Evaluate side-chains 125 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 0.0570 chunk 31 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 243 GLN A 369 GLN A 857 ASN A 975 GLN A 995 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130586 restraints weight = 7896.051| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.19 r_work: 0.3476 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7334 Z= 0.128 Angle : 0.505 5.043 9972 Z= 0.263 Chirality : 0.042 0.138 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.335 27.735 954 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.73 % Allowed : 14.01 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.29), residues: 885 helix: 2.00 (0.26), residues: 396 sheet: -0.63 (0.44), residues: 124 loop : -0.04 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 249 TYR 0.015 0.001 TYR A 294 PHE 0.012 0.001 PHE A 626 TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7334) covalent geometry : angle 0.50549 ( 9972) hydrogen bonds : bond 0.03791 ( 340) hydrogen bonds : angle 4.31981 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.252 Fit side-chains REVERT: A 71 GLU cc_start: 0.7414 (pm20) cc_final: 0.7202 (pm20) REVERT: A 142 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6109 (tm-30) REVERT: A 242 LEU cc_start: 0.8370 (mp) cc_final: 0.8077 (tt) REVERT: A 256 GLU cc_start: 0.6809 (mt-10) cc_final: 0.5875 (pm20) REVERT: A 312 GLN cc_start: 0.8149 (tp40) cc_final: 0.7852 (tp-100) REVERT: A 316 ASP cc_start: 0.7809 (m-30) cc_final: 0.7496 (m-30) REVERT: A 342 ILE cc_start: 0.7996 (mm) cc_final: 0.7686 (mm) REVERT: A 393 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7223 (mp-120) REVERT: A 586 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: A 649 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6168 (tm-30) REVERT: A 966 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6628 (tp-100) REVERT: A 971 ASP cc_start: 0.7421 (m-30) cc_final: 0.7169 (m-30) REVERT: A 995 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6638 (mp10) REVERT: A 1049 ASP cc_start: 0.7683 (m-30) cc_final: 0.7435 (m-30) REVERT: A 1059 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6853 (mtt90) outliers start: 29 outliers final: 16 residues processed: 131 average time/residue: 0.5090 time to fit residues: 70.2544 Evaluate side-chains 133 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 166 GLN A 369 GLN A 857 ASN A 975 GLN A 995 GLN A1008 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127015 restraints weight = 7944.877| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.21 r_work: 0.3435 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7334 Z= 0.167 Angle : 0.541 5.214 9972 Z= 0.281 Chirality : 0.044 0.183 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.453 27.273 954 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.60 % Allowed : 14.40 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.29), residues: 885 helix: 1.87 (0.25), residues: 394 sheet: -0.63 (0.44), residues: 124 loop : -0.02 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.017 0.001 TYR A 294 PHE 0.015 0.002 PHE A 626 TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7334) covalent geometry : angle 0.54122 ( 9972) hydrogen bonds : bond 0.04070 ( 340) hydrogen bonds : angle 4.42327 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.169 Fit side-chains REVERT: A 71 GLU cc_start: 0.7436 (pm20) cc_final: 0.7221 (pm20) REVERT: A 118 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: A 142 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6046 (tm-30) REVERT: A 242 LEU cc_start: 0.8394 (mp) cc_final: 0.8091 (tt) REVERT: A 256 GLU cc_start: 0.6895 (mt-10) cc_final: 0.5831 (pm20) REVERT: A 316 ASP cc_start: 0.7802 (m-30) cc_final: 0.7518 (m-30) REVERT: A 342 ILE cc_start: 0.8060 (mm) cc_final: 0.7622 (mm) REVERT: A 393 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7160 (mp-120) REVERT: A 586 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: A 649 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6163 (tm-30) REVERT: A 966 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6569 (tp-100) REVERT: A 971 ASP cc_start: 0.7435 (m-30) cc_final: 0.7191 (m-30) REVERT: A 995 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: A 1049 ASP cc_start: 0.7629 (m-30) cc_final: 0.7358 (m-30) REVERT: A 1059 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6907 (mtt90) outliers start: 28 outliers final: 17 residues processed: 133 average time/residue: 0.5688 time to fit residues: 79.4957 Evaluate side-chains 134 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 166 GLN A 369 GLN A 857 ASN A 995 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.163703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126685 restraints weight = 7937.240| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.20 r_work: 0.3434 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7334 Z= 0.170 Angle : 0.553 5.804 9972 Z= 0.286 Chirality : 0.044 0.264 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.488 27.146 954 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.34 % Allowed : 14.65 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.29), residues: 885 helix: 1.81 (0.25), residues: 394 sheet: -0.66 (0.44), residues: 124 loop : -0.04 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 249 TYR 0.017 0.001 TYR A 294 PHE 0.016 0.002 PHE A 626 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7334) covalent geometry : angle 0.55332 ( 9972) hydrogen bonds : bond 0.04114 ( 340) hydrogen bonds : angle 4.47357 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.216 Fit side-chains REVERT: A 118 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: A 142 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6048 (tm-30) REVERT: A 256 GLU cc_start: 0.6922 (mt-10) cc_final: 0.5886 (pm20) REVERT: A 316 ASP cc_start: 0.7802 (m-30) cc_final: 0.7519 (m-30) REVERT: A 342 ILE cc_start: 0.8093 (mm) cc_final: 0.7714 (mm) REVERT: A 393 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7127 (mp-120) REVERT: A 586 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: A 649 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6182 (tm-30) REVERT: A 966 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6624 (tp-100) REVERT: A 971 ASP cc_start: 0.7456 (m-30) cc_final: 0.7234 (m-30) REVERT: A 995 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6766 (mp10) REVERT: A 1049 ASP cc_start: 0.7619 (m-30) cc_final: 0.7341 (m-30) REVERT: A 1059 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6885 (mtt90) outliers start: 26 outliers final: 17 residues processed: 129 average time/residue: 0.5413 time to fit residues: 73.4061 Evaluate side-chains 130 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1059 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 166 GLN A 369 GLN A 857 ASN A 975 GLN A 995 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.163697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126650 restraints weight = 7884.737| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.20 r_work: 0.3436 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7334 Z= 0.170 Angle : 0.561 5.550 9972 Z= 0.290 Chirality : 0.045 0.258 1117 Planarity : 0.005 0.052 1293 Dihedral : 4.516 26.993 954 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.08 % Allowed : 15.04 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.29), residues: 885 helix: 1.80 (0.25), residues: 393 sheet: -0.63 (0.46), residues: 112 loop : -0.15 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 249 TYR 0.017 0.001 TYR A 294 PHE 0.016 0.002 PHE A 626 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7334) covalent geometry : angle 0.56108 ( 9972) hydrogen bonds : bond 0.04135 ( 340) hydrogen bonds : angle 4.48717 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2851.07 seconds wall clock time: 49 minutes 9.39 seconds (2949.39 seconds total)