Starting phenix.real_space_refine on Fri May 9 21:54:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j97_36090/05_2025/8j97_36090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j97_36090/05_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_36090/05_2025/8j97_36090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j97_36090/05_2025/8j97_36090.map" model { file = "/net/cci-nas-00/data/ceres_data/8j97_36090/05_2025/8j97_36090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j97_36090/05_2025/8j97_36090.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 11} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP: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: 3.20, per 1000 atoms: 0.83 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: 0.86 Conformation dependent library (CDL) restraints added in 592.7 milliseconds 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: 0.59 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: 1.17 Time building geometry restraints manager: 1.01 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: 0.850 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- 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 : 9.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (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 TRP 0.024 0.003 TRP H 113 HIS 0.003 0.001 HIS A 353 PHE 0.039 0.003 PHE A 115 TYR 0.022 0.002 TYR A 21 ARG 0.004 0.001 ARG H 90 Details of bonding type rmsd hydrogen bonds : bond 0.24612 ( 155) hydrogen bonds : angle 10.45562 ( 465) SS BOND : bond 0.00638 ( 2) SS BOND : angle 0.78562 ( 4) covalent geometry : bond 0.00692 ( 3944) covalent geometry : angle 0.91516 ( 5414) *********************** 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 : 0.419 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: 0.1570 time to fit residues: 17.3769 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 : 0.380 ------------------------------------------------------------------------------- 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 43 optimal weight: 0.0970 chunk 39 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 26 optimal weight: 0.0870 chunk 40 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.1334 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.145580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.134980 restraints weight = 5418.645| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.88 r_work: 0.3778 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3946 Z= 0.126 Angle : 0.627 10.792 5418 Z= 0.320 Chirality : 0.046 0.176 650 Planarity : 0.005 0.037 692 Dihedral : 5.631 45.674 582 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.97 % Allowed : 11.55 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.39), residues: 517 helix: -0.76 (1.06), residues: 24 sheet: -0.46 (0.34), residues: 250 loop : 0.13 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 113 HIS 0.001 0.000 HIS H 38 PHE 0.014 0.002 PHE A 115 TYR 0.021 0.001 TYR A 21 ARG 0.003 0.000 ARG H 90 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 155) hydrogen bonds : angle 6.20797 ( 465) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.91778 ( 4) covalent geometry : bond 0.00255 ( 3944) covalent geometry : angle 0.62693 ( 5414) *********************** 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 : 0.383 Fit side-chains REVERT: A 122 ASN cc_start: 0.8012 (t0) cc_final: 0.7430 (m-40) REVERT: A 169 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7732 (mtm180) REVERT: H 9 GLU cc_start: 0.7335 (mp0) cc_final: 0.6988 (mp0) REVERT: H 70 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7496 (mtm180) REVERT: H 86 MET cc_start: 0.7410 (mtt) cc_final: 0.7189 (mtm) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.1888 time to fit residues: 20.4542 Evaluate side-chains 91 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 10 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 1 optimal weight: 0.0770 chunk 7 optimal weight: 0.2980 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.144861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.133652 restraints weight = 5512.143| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.03 r_work: 0.3755 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3946 Z= 0.122 Angle : 0.577 10.097 5418 Z= 0.294 Chirality : 0.045 0.158 650 Planarity : 0.005 0.037 692 Dihedral : 5.242 40.352 582 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.82 % Allowed : 11.55 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.39), residues: 517 helix: -0.37 (1.07), residues: 24 sheet: -0.23 (0.34), residues: 250 loop : 0.15 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 113 HIS 0.002 0.001 HIS H 38 PHE 0.008 0.002 PHE A 80 TYR 0.018 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 155) hydrogen bonds : angle 5.57974 ( 465) SS BOND : bond 0.00348 ( 2) SS BOND : angle 0.52519 ( 4) covalent geometry : bond 0.00270 ( 3944) covalent geometry : angle 0.57659 ( 5414) *********************** 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 101 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7739 (mtm180) REVERT: H 70 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7442 (mtm180) REVERT: H 86 MET cc_start: 0.7491 (mtt) cc_final: 0.7267 (mtm) outliers start: 10 outliers final: 10 residues processed: 95 average time/residue: 0.1618 time to fit residues: 18.9309 Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.142310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.131069 restraints weight = 5633.021| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.05 r_work: 0.3726 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3946 Z= 0.170 Angle : 0.617 10.170 5418 Z= 0.313 Chirality : 0.046 0.162 650 Planarity : 0.005 0.045 692 Dihedral : 5.516 39.932 582 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.38 % Allowed : 12.96 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.39), residues: 517 helix: -0.41 (1.06), residues: 24 sheet: -0.17 (0.34), residues: 251 loop : 0.05 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.013 0.002 PHE H 105 TYR 0.023 0.002 TYR A 21 ARG 0.003 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 155) hydrogen bonds : angle 5.66150 ( 465) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.46107 ( 4) covalent geometry : bond 0.00381 ( 3944) covalent geometry : angle 0.61709 ( 5414) *********************** 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 103 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8147 (t0) cc_final: 0.7874 (t0) REVERT: A 169 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7711 (mtm180) REVERT: A 255 MET cc_start: 0.6750 (tpp) cc_final: 0.5927 (tpp) REVERT: A 347 LEU cc_start: 0.7812 (mp) cc_final: 0.7592 (mp) REVERT: L 37 TYR cc_start: 0.7014 (m-80) cc_final: 0.6785 (m-80) outliers start: 12 outliers final: 11 residues processed: 97 average time/residue: 0.1490 time to fit residues: 18.0650 Evaluate side-chains 100 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 6 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 4 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.142670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131319 restraints weight = 5737.443| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.08 r_work: 0.3727 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3946 Z= 0.149 Angle : 0.588 9.691 5418 Z= 0.298 Chirality : 0.046 0.175 650 Planarity : 0.005 0.044 692 Dihedral : 5.380 38.841 582 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.82 % Allowed : 15.21 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.39), residues: 517 helix: -0.23 (1.11), residues: 24 sheet: -0.06 (0.34), residues: 257 loop : 0.14 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.002 0.001 HIS H 38 PHE 0.011 0.002 PHE H 105 TYR 0.020 0.001 TYR A 21 ARG 0.002 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 155) hydrogen bonds : angle 5.47843 ( 465) SS BOND : bond 0.00334 ( 2) SS BOND : angle 0.51929 ( 4) covalent geometry : bond 0.00334 ( 3944) covalent geometry : angle 0.58775 ( 5414) *********************** 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 102 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6672 (m-30) cc_final: 0.6235 (m-30) REVERT: A 122 ASN cc_start: 0.8154 (t0) cc_final: 0.7869 (t0) REVERT: A 169 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7512 (mtm180) REVERT: A 255 MET cc_start: 0.6734 (tpp) cc_final: 0.5875 (tpp) REVERT: A 347 LEU cc_start: 0.7789 (mp) cc_final: 0.7581 (mp) REVERT: L 37 TYR cc_start: 0.6998 (m-80) cc_final: 0.6739 (m-80) outliers start: 10 outliers final: 10 residues processed: 96 average time/residue: 0.1465 time to fit residues: 17.6056 Evaluate side-chains 102 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 287 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 overall best weight: 0.2738 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.144027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.133079 restraints weight = 5639.603| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.99 r_work: 0.3739 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2503 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= 0.126 Angle : 0.566 9.183 5418 Z= 0.286 Chirality : 0.045 0.151 650 Planarity : 0.004 0.041 692 Dihedral : 5.163 35.839 582 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.10 % Allowed : 15.49 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.39), residues: 517 helix: -0.05 (1.12), residues: 24 sheet: 0.02 (0.34), residues: 258 loop : 0.23 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.010 0.002 PHE H 105 TYR 0.017 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 155) hydrogen bonds : angle 5.29587 ( 465) SS BOND : bond 0.00319 ( 2) SS BOND : angle 0.64310 ( 4) covalent geometry : bond 0.00280 ( 3944) covalent geometry : angle 0.56547 ( 5414) *********************** 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 106 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6598 (m-30) cc_final: 0.6123 (m-30) REVERT: A 122 ASN cc_start: 0.8121 (t0) cc_final: 0.7834 (t0) REVERT: A 169 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7496 (mtm180) REVERT: A 255 MET cc_start: 0.6733 (tpp) cc_final: 0.5915 (tpp) REVERT: L 7 GLN cc_start: 0.7411 (tt0) cc_final: 0.7148 (mt0) REVERT: L 37 TYR cc_start: 0.7022 (m-80) cc_final: 0.6735 (m-80) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.1499 time to fit residues: 18.6342 Evaluate side-chains 101 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.140754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.129903 restraints weight = 5629.621| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.94 r_work: 0.3713 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3946 Z= 0.254 Angle : 0.688 9.074 5418 Z= 0.356 Chirality : 0.049 0.222 650 Planarity : 0.006 0.053 692 Dihedral : 5.795 37.399 582 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.66 % Allowed : 17.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.39), residues: 517 helix: -0.55 (1.10), residues: 24 sheet: -0.05 (0.34), residues: 250 loop : -0.13 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 113 HIS 0.004 0.001 HIS A 295 PHE 0.038 0.003 PHE A 61 TYR 0.028 0.002 TYR A 21 ARG 0.006 0.001 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 155) hydrogen bonds : angle 5.98777 ( 465) SS BOND : bond 0.00427 ( 2) SS BOND : angle 0.59045 ( 4) covalent geometry : bond 0.00571 ( 3944) covalent geometry : angle 0.68794 ( 5414) *********************** 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 106 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6809 (m-30) cc_final: 0.6380 (m-30) REVERT: A 122 ASN cc_start: 0.8180 (t0) cc_final: 0.7857 (t0) REVERT: A 169 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7643 (mtm180) REVERT: A 255 MET cc_start: 0.6693 (tpp) cc_final: 0.6493 (tpp) REVERT: L 7 GLN cc_start: 0.7373 (tt0) cc_final: 0.7140 (mt0) REVERT: L 37 TYR cc_start: 0.7078 (m-80) cc_final: 0.6869 (m-80) outliers start: 13 outliers final: 11 residues processed: 98 average time/residue: 0.1407 time to fit residues: 17.6671 Evaluate side-chains 104 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 34 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 18 optimal weight: 0.0670 chunk 48 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 overall best weight: 0.1594 ------------------------------------------------------------------------------- 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 31 ASN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.144186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.133382 restraints weight = 5684.974| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.99 r_work: 0.3760 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3946 Z= 0.109 Angle : 0.575 8.853 5418 Z= 0.295 Chirality : 0.046 0.164 650 Planarity : 0.004 0.040 692 Dihedral : 5.081 32.726 581 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.25 % Allowed : 19.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.39), residues: 517 helix: -0.30 (1.13), residues: 24 sheet: 0.03 (0.34), residues: 258 loop : 0.04 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.017 0.002 PHE A 277 TYR 0.014 0.001 TYR A 21 ARG 0.001 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 155) hydrogen bonds : angle 5.32298 ( 465) SS BOND : bond 0.00329 ( 2) SS BOND : angle 0.84268 ( 4) covalent geometry : bond 0.00241 ( 3944) covalent geometry : angle 0.57494 ( 5414) *********************** 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 98 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6696 (m-30) cc_final: 0.6184 (m-30) REVERT: A 122 ASN cc_start: 0.8144 (t0) cc_final: 0.7870 (t0) REVERT: A 169 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7412 (mtm180) REVERT: H 86 MET cc_start: 0.7463 (mtt) cc_final: 0.7197 (mtm) REVERT: L 37 TYR cc_start: 0.6958 (m-80) cc_final: 0.6724 (m-80) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.1496 time to fit residues: 17.0643 Evaluate side-chains 96 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.142334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.131475 restraints weight = 5691.002| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.95 r_work: 0.3730 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3946 Z= 0.191 Angle : 0.647 8.879 5418 Z= 0.328 Chirality : 0.047 0.188 650 Planarity : 0.005 0.047 692 Dihedral : 5.445 35.742 581 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.82 % Allowed : 18.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.39), residues: 517 helix: -0.54 (1.10), residues: 24 sheet: -0.09 (0.33), residues: 258 loop : 0.01 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 113 HIS 0.005 0.001 HIS H 38 PHE 0.037 0.003 PHE A 61 TYR 0.023 0.002 TYR A 21 ARG 0.003 0.001 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 155) hydrogen bonds : angle 5.67034 ( 465) SS BOND : bond 0.00271 ( 2) SS BOND : angle 1.18000 ( 4) covalent geometry : bond 0.00431 ( 3944) covalent geometry : angle 0.64605 ( 5414) *********************** 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 101 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6769 (m-30) cc_final: 0.6260 (m-30) REVERT: A 122 ASN cc_start: 0.8166 (t0) cc_final: 0.7869 (t0) REVERT: A 169 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7424 (mtm180) REVERT: A 188 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7769 (tpp80) REVERT: H 33 TYR cc_start: 0.7795 (m-80) cc_final: 0.7541 (m-80) REVERT: L 7 GLN cc_start: 0.7478 (tt0) cc_final: 0.7256 (mt0) REVERT: L 37 TYR cc_start: 0.7014 (m-80) cc_final: 0.6781 (m-80) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.1500 time to fit residues: 18.0471 Evaluate side-chains 100 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 287 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 34 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 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.141414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130093 restraints weight = 5746.301| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.09 r_work: 0.3706 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3946 Z= 0.202 Angle : 0.657 9.303 5418 Z= 0.336 Chirality : 0.048 0.193 650 Planarity : 0.005 0.049 692 Dihedral : 5.560 36.179 581 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.25 % Allowed : 18.59 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.39), residues: 517 helix: -0.56 (1.10), residues: 24 sheet: -0.06 (0.34), residues: 251 loop : -0.17 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 113 HIS 0.005 0.001 HIS H 38 PHE 0.019 0.002 PHE A 277 TYR 0.023 0.002 TYR A 21 ARG 0.005 0.001 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 155) hydrogen bonds : angle 5.78705 ( 465) SS BOND : bond 0.00408 ( 2) SS BOND : angle 1.25024 ( 4) covalent geometry : bond 0.00458 ( 3944) covalent geometry : angle 0.65680 ( 5414) ********************** 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 97 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6799 (m-30) cc_final: 0.6258 (m-30) REVERT: A 122 ASN cc_start: 0.8176 (t0) cc_final: 0.7846 (t0) REVERT: A 169 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7438 (mtm180) REVERT: A 188 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7857 (tpp80) REVERT: H 33 TYR cc_start: 0.7732 (m-80) cc_final: 0.7517 (m-80) REVERT: L 7 GLN cc_start: 0.7586 (tt0) cc_final: 0.7357 (mt0) REVERT: L 37 TYR cc_start: 0.7073 (m-80) cc_final: 0.6840 (m-80) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.1472 time to fit residues: 17.1001 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 34 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 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 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 = 0.3935 r_free = 0.3935 target = 0.141323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130568 restraints weight = 5668.978| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.95 r_work: 0.3725 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3946 Z= 0.207 Angle : 0.658 8.969 5418 Z= 0.336 Chirality : 0.048 0.188 650 Planarity : 0.005 0.051 692 Dihedral : 5.612 36.151 581 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.54 % Allowed : 17.75 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.39), residues: 517 helix: -0.60 (1.10), residues: 24 sheet: -0.17 (0.34), residues: 251 loop : -0.19 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 113 HIS 0.004 0.001 HIS H 38 PHE 0.039 0.003 PHE A 61 TYR 0.023 0.002 TYR A 21 ARG 0.004 0.001 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 155) hydrogen bonds : angle 5.86357 ( 465) SS BOND : bond 0.00423 ( 2) SS BOND : angle 1.29294 ( 4) covalent geometry : bond 0.00468 ( 3944) covalent geometry : angle 0.65689 ( 5414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.11 seconds wall clock time: 41 minutes 29.44 seconds (2489.44 seconds total)