Starting phenix.real_space_refine on Sun Apr 27 00:31:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j97_36090/04_2025/8j97_36090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j97_36090/04_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_36090/04_2025/8j97_36090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j97_36090/04_2025/8j97_36090.map" model { file = "/net/cci-nas-00/data/ceres_data/8j97_36090/04_2025/8j97_36090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j97_36090/04_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-5669/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: 3.44, per 1000 atoms: 0.89 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: 0.98 Conformation dependent library (CDL) restraints added in 494.9 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: 0.63 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: 1.23 Time building geometry restraints manager: 1.16 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: 1.330 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.010 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- 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 : 0.393 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: 0.1565 time to fit residues: 17.3502 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 : 0.378 ------------------------------------------------------------------------------- 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 = 0.145581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.134981 restraints weight = 5418.631| |-----------------------------------------------------------------------------| 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 10.789 5418 Z= 0.320 Chirality : 0.046 0.176 650 Planarity : 0.005 0.037 692 Dihedral : 5.631 45.673 582 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 6.20796 ( 465) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.91783 ( 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 : 0.592 Fit side-chains REVERT: A 122 ASN cc_start: 0.8011 (t0) cc_final: 0.7429 (m-40) REVERT: A 169 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7731 (mtm180) REVERT: H 9 GLU cc_start: 0.7332 (mp0) cc_final: 0.6986 (mp0) REVERT: H 70 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7495 (mtm180) REVERT: H 86 MET cc_start: 0.7408 (mtt) cc_final: 0.7188 (mtm) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.2223 time to fit residues: 24.3193 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 : 0.436 ------------------------------------------------------------------------------- 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: 0.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.0050 chunk 1 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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** L 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131710 restraints weight = 5463.944| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.96 r_work: 0.3731 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3946 Z= 0.177 Angle : 0.632 10.464 5418 Z= 0.325 Chirality : 0.047 0.154 650 Planarity : 0.005 0.044 692 Dihedral : 5.717 42.202 582 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.66 % Allowed : 11.27 % 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 (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: -0.44 (0.39), residues: 517 helix: -0.71 (1.04), residues: 24 sheet: -0.38 (0.34), residues: 252 loop : 0.08 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 113 HIS 0.003 0.001 HIS H 38 PHE 0.013 0.002 PHE H 105 TYR 0.023 0.002 TYR A 21 ARG 0.003 0.001 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 155) hydrogen bonds : angle 5.97621 ( 465) SS BOND : bond 0.00419 ( 2) SS BOND : angle 0.45262 ( 4) covalent geometry : bond 0.00396 ( 3944) covalent geometry : angle 0.63168 ( 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: 13 poor density : 88 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7695 (mtm180) REVERT: H 86 MET cc_start: 0.7536 (mtt) cc_final: 0.7244 (mtm) REVERT: L 7 GLN cc_start: 0.7358 (tt0) cc_final: 0.7050 (mt0) REVERT: L 37 TYR cc_start: 0.7031 (m-80) cc_final: 0.6749 (m-80) outliers start: 13 outliers final: 12 residues processed: 95 average time/residue: 0.1975 time to fit residues: 22.9906 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 : 0.500 ------------------------------------------------------------------------------- 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 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.140316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129665 restraints weight = 5594.317| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.91 r_work: 0.3713 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3946 Z= 0.241 Angle : 0.687 9.915 5418 Z= 0.354 Chirality : 0.049 0.202 650 Planarity : 0.006 0.054 692 Dihedral : 6.004 39.711 582 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.94 % Allowed : 12.11 % Favored : 83.94 % 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: -0.57 (0.39), residues: 517 helix: -0.78 (1.06), residues: 24 sheet: -0.39 (0.35), residues: 249 loop : -0.12 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 113 HIS 0.003 0.001 HIS A 210 PHE 0.017 0.003 PHE H 105 TYR 0.027 0.002 TYR A 21 ARG 0.005 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 155) hydrogen bonds : angle 6.20705 ( 465) SS BOND : bond 0.00453 ( 2) SS BOND : angle 0.51991 ( 4) covalent geometry : bond 0.00541 ( 3944) covalent geometry : angle 0.68730 ( 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 105 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.891 Fit side-chains REVERT: H 9 GLU cc_start: 0.7356 (mp0) cc_final: 0.6944 (mp0) REVERT: L 87 TYR cc_start: 0.6273 (m-80) cc_final: 0.6063 (m-80) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 0.1854 time to fit residues: 23.0142 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 : 0.373 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.139705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.129017 restraints weight = 5739.101| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.94 r_work: 0.3701 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3946 Z= 0.268 Angle : 0.705 8.324 5418 Z= 0.365 Chirality : 0.049 0.165 650 Planarity : 0.006 0.058 692 Dihedral : 6.140 39.061 581 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.38 % Allowed : 15.21 % 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: -0.71 (0.38), residues: 517 helix: -0.95 (1.08), residues: 25 sheet: -0.45 (0.34), residues: 249 loop : -0.26 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 113 HIS 0.003 0.001 HIS A 295 PHE 0.018 0.002 PHE H 105 TYR 0.029 0.002 TYR A 21 ARG 0.003 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 155) hydrogen bonds : angle 6.34286 ( 465) SS BOND : bond 0.00466 ( 2) SS BOND : angle 0.79475 ( 4) covalent geometry : bond 0.00602 ( 3944) covalent geometry : angle 0.70517 ( 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 97 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.409 Fit side-chains REVERT: A 26 ASP cc_start: 0.6447 (m-30) cc_final: 0.5955 (m-30) REVERT: A 169 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7724 (mtm180) REVERT: A 255 MET cc_start: 0.6570 (tpp) cc_final: 0.6351 (tpp) outliers start: 12 outliers final: 11 residues processed: 88 average time/residue: 0.1532 time to fit residues: 16.7938 Evaluate side-chains 95 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.141454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.130731 restraints weight = 5710.501| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.97 r_work: 0.3714 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2415 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= 0.184 Angle : 0.632 8.755 5418 Z= 0.325 Chirality : 0.047 0.155 650 Planarity : 0.005 0.051 692 Dihedral : 5.764 38.430 581 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.10 % Allowed : 16.06 % 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 (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: -0.65 (0.39), residues: 517 helix: -0.82 (1.05), residues: 25 sheet: -0.38 (0.34), residues: 250 loop : -0.25 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 113 HIS 0.003 0.001 HIS A 353 PHE 0.013 0.002 PHE H 105 TYR 0.022 0.002 TYR A 21 ARG 0.001 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 155) hydrogen bonds : angle 5.97805 ( 465) SS BOND : bond 0.00473 ( 2) SS BOND : angle 0.70792 ( 4) covalent geometry : bond 0.00412 ( 3944) covalent geometry : angle 0.63177 ( 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 103 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.557 Fit side-chains REVERT: A 26 ASP cc_start: 0.6450 (m-30) cc_final: 0.5988 (m-30) REVERT: A 169 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7694 (mtm180) REVERT: A 255 MET cc_start: 0.6610 (tpp) cc_final: 0.6399 (tpp) REVERT: H 9 GLU cc_start: 0.7390 (mp0) cc_final: 0.6912 (mp0) outliers start: 11 outliers final: 11 residues processed: 95 average time/residue: 0.1745 time to fit residues: 21.0053 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 : 0.693 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.140286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.129705 restraints weight = 5682.604| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.92 r_work: 0.3709 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3946 Z= 0.239 Angle : 0.682 8.168 5418 Z= 0.354 Chirality : 0.049 0.175 650 Planarity : 0.006 0.056 692 Dihedral : 5.947 37.979 581 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.66 % Allowed : 17.18 % 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: -0.69 (0.39), residues: 517 helix: -0.81 (1.08), residues: 24 sheet: -0.40 (0.34), residues: 247 loop : -0.30 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 113 HIS 0.003 0.001 HIS A 295 PHE 0.017 0.002 PHE H 105 TYR 0.026 0.002 TYR A 21 ARG 0.003 0.001 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 155) hydrogen bonds : angle 6.17629 ( 465) SS BOND : bond 0.00437 ( 2) SS BOND : angle 0.89245 ( 4) covalent geometry : bond 0.00536 ( 3944) covalent geometry : angle 0.68188 ( 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 103 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.418 Fit side-chains REVERT: A 26 ASP cc_start: 0.6468 (m-30) cc_final: 0.5975 (m-30) REVERT: A 169 ARG cc_start: 0.8029 (mtp180) cc_final: 0.7701 (mtm180) REVERT: A 255 MET cc_start: 0.6570 (tpp) cc_final: 0.6367 (tpp) outliers start: 13 outliers final: 11 residues processed: 94 average time/residue: 0.2117 time to fit residues: 24.9737 Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 0.0270 chunk 32 optimal weight: 0.0670 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.142185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131105 restraints weight = 5747.600| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.07 r_work: 0.3721 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3946 Z= 0.145 Angle : 0.610 8.498 5418 Z= 0.314 Chirality : 0.046 0.170 650 Planarity : 0.005 0.048 692 Dihedral : 5.512 35.626 581 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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 (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: -0.65 (0.39), residues: 517 helix: -0.63 (1.08), residues: 24 sheet: -0.35 (0.34), residues: 253 loop : -0.32 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 113 HIS 0.003 0.001 HIS A 353 PHE 0.039 0.002 PHE A 61 TYR 0.018 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 155) hydrogen bonds : angle 5.72076 ( 465) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.94146 ( 4) covalent geometry : bond 0.00325 ( 3944) covalent geometry : angle 0.60955 ( 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 96 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.404 Fit side-chains REVERT: A 26 ASP cc_start: 0.6490 (m-30) cc_final: 0.6037 (m-30) REVERT: A 169 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7680 (mtm180) REVERT: H 9 GLU cc_start: 0.7370 (mp0) cc_final: 0.6858 (mp0) REVERT: L 37 TYR cc_start: 0.6838 (m-80) cc_final: 0.6625 (m-80) outliers start: 10 outliers final: 9 residues processed: 91 average time/residue: 0.1711 time to fit residues: 19.3797 Evaluate side-chains 94 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 18 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.142361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130945 restraints weight = 5788.075| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.13 r_work: 0.3708 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3946 Z= 0.154 Angle : 0.618 8.220 5418 Z= 0.314 Chirality : 0.046 0.170 650 Planarity : 0.005 0.048 692 Dihedral : 5.462 34.414 581 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.25 % Allowed : 20.56 % Favored : 77.18 % 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: -0.53 (0.39), residues: 517 helix: -0.53 (1.10), residues: 24 sheet: -0.26 (0.34), residues: 254 loop : -0.25 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 113 HIS 0.003 0.001 HIS A 353 PHE 0.014 0.002 PHE A 277 TYR 0.019 0.001 TYR A 21 ARG 0.003 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 155) hydrogen bonds : angle 5.66536 ( 465) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.84092 ( 4) covalent geometry : bond 0.00349 ( 3944) covalent geometry : angle 0.61740 ( 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 93 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.407 Fit side-chains REVERT: A 26 ASP cc_start: 0.6544 (m-30) cc_final: 0.6100 (m-30) REVERT: A 169 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7680 (mtm180) outliers start: 8 outliers final: 7 residues processed: 89 average time/residue: 0.1506 time to fit residues: 16.7069 Evaluate side-chains 91 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 0.0000 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 chunk 46 optimal weight: 0.0270 overall best weight: 0.2100 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.144328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.133687 restraints weight = 5700.952| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.94 r_work: 0.3751 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3946 Z= 0.117 Angle : 0.582 8.599 5418 Z= 0.295 Chirality : 0.045 0.161 650 Planarity : 0.005 0.043 692 Dihedral : 5.041 29.489 581 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.97 % Allowed : 20.56 % Favored : 77.46 % 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: -0.37 (0.39), residues: 517 helix: -0.38 (1.11), residues: 24 sheet: -0.18 (0.33), residues: 258 loop : -0.13 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.035 0.002 PHE A 61 TYR 0.015 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 155) hydrogen bonds : angle 5.34064 ( 465) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.59057 ( 4) covalent geometry : bond 0.00267 ( 3944) covalent geometry : angle 0.58151 ( 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: 7 poor density : 90 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6453 (m-30) cc_final: 0.6050 (m-30) REVERT: A 169 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7640 (mtm180) REVERT: H 86 MET cc_start: 0.7448 (mtt) cc_final: 0.7175 (mtm) outliers start: 7 outliers final: 7 residues processed: 94 average time/residue: 0.1535 time to fit residues: 18.0271 Evaluate side-chains 95 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 L residue 57 SER Chi-restraints excluded: chain L residue 105 VAL 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: 0.8980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 20 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.132200 restraints weight = 5684.316| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.94 r_work: 0.3731 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2941 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= 0.164 Angle : 0.615 8.453 5418 Z= 0.314 Chirality : 0.046 0.164 650 Planarity : 0.005 0.047 692 Dihedral : 5.286 31.270 581 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.97 % Allowed : 21.13 % Favored : 76.90 % 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: -0.45 (0.39), residues: 517 helix: -0.50 (1.09), residues: 24 sheet: -0.24 (0.33), residues: 259 loop : -0.14 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 113 HIS 0.003 0.001 HIS A 353 PHE 0.012 0.002 PHE A 277 TYR 0.021 0.001 TYR A 21 ARG 0.003 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 155) hydrogen bonds : angle 5.53012 ( 465) SS BOND : bond 0.00382 ( 2) SS BOND : angle 1.13732 ( 4) covalent geometry : bond 0.00372 ( 3944) covalent geometry : angle 0.61397 ( 5414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.19 seconds wall clock time: 49 minutes 26.90 seconds (2966.90 seconds total)