Starting phenix.real_space_refine on Fri Aug 22 14:17:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j97_36090/08_2025/8j97_36090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j97_36090/08_2025/8j97_36090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j97_36090/08_2025/8j97_36090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j97_36090/08_2025/8j97_36090.map" model { file = "/net/cci-nas-00/data/ceres_data/8j97_36090/08_2025/8j97_36090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j97_36090/08_2025/8j97_36090.cif" } resolution = 3.2 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= 0.011 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 13 5.16 5 C 2466 2.51 5 N 649 2.21 5 O 731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3863 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2196 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 289} Chain breaks: 6 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 11, 'TYR:plan': 5, 'ARG:plan': 11, 'PHE:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 182 Chain: "H" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 864 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 729 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 1.10, per 1000 atoms: 0.28 Number of scatterers: 3863 At special positions: 0 Unit cell: (55.2967, 103.85, 83.6194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 4 15.00 O 731 8.00 N 649 7.00 C 2466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 0.24 Conformation dependent library (CDL) restraints added in 147.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 12 sheets defined 6.6% alpha, 51.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.977A pdb=" N ARG A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 80 removed outlier: 3.792A pdb=" N ASN H 80 " --> pdb=" O THR H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.026A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 118 removed outlier: 3.530A pdb=" N PHE A 117 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 7.304A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 55 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 57 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN A 83 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N CYS A 59 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL A 81 " --> pdb=" O CYS A 59 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 61 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 79 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 7.304A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.557A pdb=" N ARG A 188 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 197 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.557A pdb=" N ARG A 188 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 197 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.076A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER A 330 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 228 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.544A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.555A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.555A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.282A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.282A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 465 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: 0.60 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 627 1.32 - 1.44: 1050 1.44 - 1.56: 2239 1.56 - 1.69: 11 1.69 - 1.81: 17 Bond restraints: 3944 Sorted by residual: bond pdb=" OG1 TPO V 307 " pdb=" P TPO V 307 " ideal model delta sigma weight residual 1.717 1.599 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" OG1 TPO V 310 " pdb=" P TPO V 310 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O1P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O2P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O3P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 5322 2.88 - 5.75: 73 5.75 - 8.63: 12 8.63 - 11.51: 5 11.51 - 14.38: 2 Bond angle restraints: 5414 Sorted by residual: angle pdb=" C ASP A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta sigma weight residual 121.97 129.37 -7.40 1.00e+00 1.00e+00 5.48e+01 angle pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " pdb=" CG PHE A 115 " ideal model delta sigma weight residual 113.80 121.12 -7.32 1.00e+00 1.00e+00 5.35e+01 angle pdb=" C PRO A 114 " pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 111.56 101.98 9.58 1.65e+00 3.67e-01 3.37e+01 angle pdb=" N VAL A 343 " pdb=" CA VAL A 343 " pdb=" CB VAL A 343 " ideal model delta sigma weight residual 109.84 116.68 -6.84 1.32e+00 5.74e-01 2.68e+01 angle pdb=" CB TPO V 307 " pdb=" OG1 TPO V 307 " pdb=" P TPO V 307 " ideal model delta sigma weight residual 119.31 104.93 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 5409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2140 17.85 - 35.70: 136 35.70 - 53.55: 29 53.55 - 71.40: 1 71.40 - 89.25: 5 Dihedral angle restraints: 2311 sinusoidal: 732 harmonic: 1579 Sorted by residual: dihedral pdb=" CA LYS A 229 " pdb=" C LYS A 229 " pdb=" N LYS A 230 " pdb=" CA LYS A 230 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ASP A 342 " pdb=" C ASP A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLN L 90 " pdb=" C GLN L 90 " pdb=" N GLN L 91 " pdb=" CA GLN L 91 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 2308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 456 0.046 - 0.091: 140 0.091 - 0.137: 48 0.137 - 0.183: 5 0.183 - 0.228: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CB VAL A 343 " pdb=" CA VAL A 343 " pdb=" CG1 VAL A 343 " pdb=" CG2 VAL A 343 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TYR A 113 " pdb=" N TYR A 113 " pdb=" C TYR A 113 " pdb=" CB TYR A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 647 not shown) Planarity restraints: 692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 115 " -0.024 2.00e-02 2.50e+03 1.77e-02 5.46e+00 pdb=" CG PHE A 115 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 115 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 115 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 115 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 115 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 115 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 353 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 354 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 181 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 182 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " 0.022 5.00e-02 4.00e+02 ... (remaining 689 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 948 2.79 - 3.32: 3377 3.32 - 3.85: 6084 3.85 - 4.37: 6966 4.37 - 4.90: 12439 Nonbonded interactions: 29814 Sorted by model distance: nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.266 3.040 nonbonded pdb=" NH2 ARG A 7 " pdb=" OG SEP V 309 " model vdw 2.314 3.120 nonbonded pdb=" O THR A 221 " pdb=" OG1 THR A 221 " model vdw 2.326 3.040 nonbonded pdb=" NH2 ARG A 25 " pdb=" O VAL A 167 " model vdw 2.331 3.120 nonbonded pdb=" OD1 ASN H 31 " pdb=" N VAL H 32 " model vdw 2.347 3.120 ... (remaining 29809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.007 0.118 3946 Z= 0.343 Angle : 0.915 14.385 5418 Z= 0.483 Chirality : 0.050 0.228 650 Planarity : 0.006 0.053 692 Dihedral : 13.201 89.250 1285 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.28 % Allowed : 10.42 % Favored : 89.30 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -1.02 (0.37), residues: 517 helix: -1.09 (1.28), residues: 18 sheet: -0.98 (0.34), residues: 237 loop : -0.15 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 90 TYR 0.022 0.002 TYR A 21 PHE 0.039 0.003 PHE A 115 TRP 0.024 0.003 TRP H 113 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 3944) covalent geometry : angle 0.91516 ( 5414) SS BOND : bond 0.00638 ( 2) SS BOND : angle 0.78562 ( 4) hydrogen bonds : bond 0.24612 ( 155) hydrogen bonds : angle 10.45562 ( 465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.100 Fit side-chains REVERT: A 169 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7611 (mtm180) REVERT: H 33 TYR cc_start: 0.7978 (m-80) cc_final: 0.7644 (m-80) REVERT: H 86 MET cc_start: 0.7488 (mtt) cc_final: 0.7278 (mtm) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.0598 time to fit residues: 6.6666 Evaluate side-chains 88 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 overall best weight: 0.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.145369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134606 restraints weight = 5532.283| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.91 r_work: 0.3775 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3946 Z= 0.119 Angle : 0.632 10.913 5418 Z= 0.323 Chirality : 0.046 0.174 650 Planarity : 0.005 0.037 692 Dihedral : 5.695 46.217 582 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.97 % Allowed : 11.27 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.50 (0.39), residues: 517 helix: -0.75 (1.06), residues: 24 sheet: -0.49 (0.34), residues: 251 loop : 0.12 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 90 TYR 0.022 0.001 TYR A 21 PHE 0.011 0.002 PHE A 115 TRP 0.012 0.002 TRP H 113 HIS 0.002 0.000 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 3944) covalent geometry : angle 0.63220 ( 5414) SS BOND : bond 0.00337 ( 2) SS BOND : angle 0.90866 ( 4) hydrogen bonds : bond 0.04049 ( 155) hydrogen bonds : angle 6.24070 ( 465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.087 Fit side-chains REVERT: A 28 VAL cc_start: 0.7673 (m) cc_final: 0.7468 (p) REVERT: A 169 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7728 (mtm180) REVERT: H 9 GLU cc_start: 0.7316 (mp0) cc_final: 0.6968 (mp0) REVERT: H 70 ARG cc_start: 0.7906 (mtm110) cc_final: 0.7501 (mtm180) REVERT: H 86 MET cc_start: 0.7419 (mtt) cc_final: 0.7194 (mtm) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.0844 time to fit residues: 9.1294 Evaluate side-chains 90 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.0980 chunk 26 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132249 restraints weight = 5487.187| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.89 r_work: 0.3741 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3946 Z= 0.165 Angle : 0.622 10.682 5418 Z= 0.319 Chirality : 0.046 0.155 650 Planarity : 0.005 0.044 692 Dihedral : 5.659 41.383 582 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.38 % Allowed : 11.55 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.38 (0.39), residues: 517 helix: -0.67 (1.04), residues: 24 sheet: -0.29 (0.34), residues: 250 loop : 0.04 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 7 TYR 0.022 0.002 TYR A 21 PHE 0.012 0.002 PHE H 105 TRP 0.014 0.002 TRP H 113 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3944) covalent geometry : angle 0.62255 ( 5414) SS BOND : bond 0.00432 ( 2) SS BOND : angle 0.47019 ( 4) hydrogen bonds : bond 0.04257 ( 155) hydrogen bonds : angle 5.89398 ( 465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8101 (t0) cc_final: 0.7836 (t0) REVERT: A 169 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7674 (mtm180) REVERT: H 86 MET cc_start: 0.7539 (mtt) cc_final: 0.7259 (mtm) REVERT: L 7 GLN cc_start: 0.7312 (tt0) cc_final: 0.7013 (mt0) REVERT: L 37 TYR cc_start: 0.7011 (m-80) cc_final: 0.6718 (m-80) outliers start: 12 outliers final: 12 residues processed: 94 average time/residue: 0.0749 time to fit residues: 8.7715 Evaluate side-chains 98 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 299 ASN ** 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 = 0.3917 r_free = 0.3917 target = 0.140151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129532 restraints weight = 5599.723| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.91 r_work: 0.3711 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3946 Z= 0.248 Angle : 0.690 10.386 5418 Z= 0.356 Chirality : 0.049 0.195 650 Planarity : 0.006 0.055 692 Dihedral : 6.029 39.549 582 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.23 % Allowed : 12.39 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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 (0.39), residues: 517 helix: -1.02 (1.03), residues: 25 sheet: -0.38 (0.35), residues: 249 loop : -0.13 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 67 TYR 0.028 0.002 TYR A 21 PHE 0.017 0.003 PHE H 105 TRP 0.020 0.002 TRP H 113 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 3944) covalent geometry : angle 0.69037 ( 5414) SS BOND : bond 0.00447 ( 2) SS BOND : angle 0.53068 ( 4) hydrogen bonds : bond 0.04422 ( 155) hydrogen bonds : angle 6.24358 ( 465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.147 Fit side-chains REVERT: A 122 ASN cc_start: 0.8157 (t0) cc_final: 0.7831 (t0) REVERT: A 255 MET cc_start: 0.6677 (tpp) cc_final: 0.5971 (tpp) REVERT: L 87 TYR cc_start: 0.6254 (m-80) cc_final: 0.6048 (m-80) outliers start: 15 outliers final: 12 residues processed: 96 average time/residue: 0.0662 time to fit residues: 8.1178 Evaluate side-chains 101 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** 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 = 0.3926 r_free = 0.3926 target = 0.140731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130289 restraints weight = 5583.077| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.90 r_work: 0.3720 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3946 Z= 0.205 Angle : 0.643 9.376 5418 Z= 0.331 Chirality : 0.047 0.157 650 Planarity : 0.005 0.052 692 Dihedral : 5.796 38.941 581 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.38 % Allowed : 15.77 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.61 (0.38), residues: 517 helix: -0.83 (1.06), residues: 25 sheet: -0.37 (0.34), residues: 250 loop : -0.20 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.024 0.002 TYR A 21 PHE 0.015 0.002 PHE H 105 TRP 0.016 0.002 TRP H 113 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 3944) covalent geometry : angle 0.64303 ( 5414) SS BOND : bond 0.00444 ( 2) SS BOND : angle 0.68914 ( 4) hydrogen bonds : bond 0.04024 ( 155) hydrogen bonds : angle 6.02470 ( 465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.144 Fit side-chains REVERT: A 26 ASP cc_start: 0.6454 (m-30) cc_final: 0.6023 (m-30) REVERT: A 122 ASN cc_start: 0.8118 (t0) cc_final: 0.7807 (t0) REVERT: A 169 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7694 (mtm180) REVERT: A 255 MET cc_start: 0.6699 (tpp) cc_final: 0.5863 (tpp) REVERT: H 9 GLU cc_start: 0.7388 (mp0) cc_final: 0.6955 (mp0) REVERT: L 87 TYR cc_start: 0.6299 (m-80) cc_final: 0.6036 (m-80) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.0719 time to fit residues: 8.6110 Evaluate side-chains 101 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.142311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131277 restraints weight = 5645.145| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.99 r_work: 0.3709 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3946 Z= 0.175 Angle : 0.620 9.153 5418 Z= 0.317 Chirality : 0.046 0.159 650 Planarity : 0.005 0.048 692 Dihedral : 5.591 38.110 581 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.82 % Allowed : 16.34 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.50 (0.39), residues: 517 helix: -0.75 (1.06), residues: 25 sheet: -0.30 (0.34), residues: 250 loop : -0.14 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.022 0.002 TYR A 21 PHE 0.013 0.002 PHE H 105 TRP 0.013 0.002 TRP H 113 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3944) covalent geometry : angle 0.61969 ( 5414) SS BOND : bond 0.00406 ( 2) SS BOND : angle 0.61155 ( 4) hydrogen bonds : bond 0.03790 ( 155) hydrogen bonds : angle 5.81211 ( 465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.146 Fit side-chains REVERT: A 26 ASP cc_start: 0.6603 (m-30) cc_final: 0.6208 (m-30) REVERT: A 122 ASN cc_start: 0.8151 (t0) cc_final: 0.7849 (t0) REVERT: A 169 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7668 (mtm180) REVERT: A 255 MET cc_start: 0.6749 (tpp) cc_final: 0.6010 (tpp) REVERT: A 347 LEU cc_start: 0.7793 (mp) cc_final: 0.7580 (mp) REVERT: H 9 GLU cc_start: 0.7403 (mp0) cc_final: 0.6915 (mp0) outliers start: 10 outliers final: 10 residues processed: 97 average time/residue: 0.0724 time to fit residues: 8.7999 Evaluate side-chains 100 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 18 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.3688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** 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 = 0.3944 r_free = 0.3944 target = 0.142231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131505 restraints weight = 5748.851| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.98 r_work: 0.3729 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3946 Z= 0.157 Angle : 0.607 8.966 5418 Z= 0.313 Chirality : 0.046 0.157 650 Planarity : 0.005 0.045 692 Dihedral : 5.459 36.690 581 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.82 % Allowed : 16.90 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.43 (0.39), residues: 517 helix: -0.55 (1.09), residues: 24 sheet: -0.25 (0.34), residues: 252 loop : -0.09 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 25 TYR 0.019 0.002 TYR A 21 PHE 0.014 0.002 PHE A 277 TRP 0.012 0.002 TRP H 113 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3944) covalent geometry : angle 0.60650 ( 5414) SS BOND : bond 0.00434 ( 2) SS BOND : angle 0.80775 ( 4) hydrogen bonds : bond 0.03652 ( 155) hydrogen bonds : angle 5.70069 ( 465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6668 (m-30) cc_final: 0.6311 (m-30) REVERT: A 122 ASN cc_start: 0.8197 (t0) cc_final: 0.7938 (t0) REVERT: A 169 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7666 (mtm180) REVERT: A 255 MET cc_start: 0.6745 (tpp) cc_final: 0.6540 (tpp) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.0736 time to fit residues: 8.6767 Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.0060 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** 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 = 0.3953 r_free = 0.3953 target = 0.142784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131911 restraints weight = 5617.305| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.99 r_work: 0.3735 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3946 Z= 0.143 Angle : 0.597 8.984 5418 Z= 0.306 Chirality : 0.046 0.166 650 Planarity : 0.005 0.043 692 Dihedral : 5.323 34.165 581 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.38 % Allowed : 17.18 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.47 (0.39), residues: 517 helix: -0.49 (1.10), residues: 24 sheet: -0.27 (0.33), residues: 259 loop : -0.14 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 25 TYR 0.018 0.001 TYR A 21 PHE 0.024 0.002 PHE A 61 TRP 0.011 0.001 TRP H 113 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3944) covalent geometry : angle 0.59637 ( 5414) SS BOND : bond 0.00492 ( 2) SS BOND : angle 0.92469 ( 4) hydrogen bonds : bond 0.03473 ( 155) hydrogen bonds : angle 5.54938 ( 465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6645 (m-30) cc_final: 0.6197 (m-30) REVERT: A 122 ASN cc_start: 0.8154 (t0) cc_final: 0.7906 (t0) REVERT: A 169 ARG cc_start: 0.7920 (mtp180) cc_final: 0.7540 (mtm180) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.0675 time to fit residues: 8.3726 Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.0270 chunk 8 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 overall best weight: 0.1752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** 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 = 0.3978 r_free = 0.3978 target = 0.144746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.133344 restraints weight = 5775.860| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.12 r_work: 0.3753 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3946 Z= 0.109 Angle : 0.576 8.756 5418 Z= 0.290 Chirality : 0.045 0.157 650 Planarity : 0.004 0.040 692 Dihedral : 4.953 29.506 581 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.25 % Allowed : 18.87 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.39), residues: 517 helix: -0.30 (1.13), residues: 24 sheet: -0.13 (0.33), residues: 259 loop : 0.02 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 90 TYR 0.014 0.001 TYR A 21 PHE 0.027 0.002 PHE A 61 TRP 0.009 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3944) covalent geometry : angle 0.57576 ( 5414) SS BOND : bond 0.00367 ( 2) SS BOND : angle 0.70736 ( 4) hydrogen bonds : bond 0.03190 ( 155) hydrogen bonds : angle 5.29295 ( 465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6637 (m-30) cc_final: 0.6219 (m-30) REVERT: A 122 ASN cc_start: 0.8089 (t0) cc_final: 0.7856 (t0) REVERT: A 169 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7528 (mtm180) REVERT: A 255 MET cc_start: 0.6692 (tpp) cc_final: 0.6442 (tpp) outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 0.0718 time to fit residues: 8.5255 Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 10 optimal weight: 0.0270 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** 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 = 0.3986 r_free = 0.3986 target = 0.146820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.135656 restraints weight = 5736.967| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.97 r_work: 0.3761 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3946 Z= 0.119 Angle : 0.583 9.013 5418 Z= 0.293 Chirality : 0.045 0.155 650 Planarity : 0.004 0.039 692 Dihedral : 4.872 27.554 581 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.54 % Allowed : 18.87 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.20 (0.39), residues: 517 helix: -0.26 (1.13), residues: 24 sheet: -0.13 (0.33), residues: 260 loop : 0.09 (0.45), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.016 0.001 TYR A 21 PHE 0.036 0.002 PHE A 61 TRP 0.011 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3944) covalent geometry : angle 0.58269 ( 5414) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.60215 ( 4) hydrogen bonds : bond 0.03146 ( 155) hydrogen bonds : angle 5.26365 ( 465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6577 (m-30) cc_final: 0.6177 (m-30) REVERT: A 122 ASN cc_start: 0.8061 (t0) cc_final: 0.7824 (t0) REVERT: A 169 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7519 (mtm180) outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.0610 time to fit residues: 7.2553 Evaluate side-chains 98 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 0.0470 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 0.0470 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 32 optimal weight: 0.0980 overall best weight: 0.1376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136120 restraints weight = 5704.045| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.96 r_work: 0.3779 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3946 Z= 0.103 Angle : 0.561 8.869 5418 Z= 0.285 Chirality : 0.044 0.154 650 Planarity : 0.004 0.038 692 Dihedral : 4.586 23.804 581 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.82 % Allowed : 18.87 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.39), residues: 517 helix: -0.12 (1.15), residues: 24 sheet: -0.11 (0.33), residues: 260 loop : 0.18 (0.45), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.013 0.001 TYR A 21 PHE 0.009 0.001 PHE A 277 TRP 0.009 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3944) covalent geometry : angle 0.56126 ( 5414) SS BOND : bond 0.00086 ( 2) SS BOND : angle 0.73578 ( 4) hydrogen bonds : bond 0.02958 ( 155) hydrogen bonds : angle 5.08706 ( 465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1179.40 seconds wall clock time: 20 minutes 52.83 seconds (1252.83 seconds total)