Starting phenix.real_space_refine on Sat Jun 7 07:43:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u56_41913/06_2025/8u56_41913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u56_41913/06_2025/8u56_41913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u56_41913/06_2025/8u56_41913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u56_41913/06_2025/8u56_41913.map" model { file = "/net/cci-nas-00/data/ceres_data/8u56_41913/06_2025/8u56_41913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u56_41913/06_2025/8u56_41913.cif" } resolution = 2.75 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= -0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5814 2.51 5 N 1300 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4253 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 521} Chain breaks: 5 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'LMN': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B Time building chain proxies: 8.26, per 1000 atoms: 0.96 Number of scatterers: 8588 At special positions: 0 Unit cell: (101.215, 124.276, 75.5908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1418 8.00 N 1300 7.00 C 5814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 91.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.631A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 125 Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 164 through 194 removed outlier: 3.901A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 238 through 265 removed outlier: 3.672A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 326 through 336 removed outlier: 4.120A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.617A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.576A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 473 Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.994A pdb=" N ILE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix removed outlier: 3.729A pdb=" N VAL A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 543 Processing helix chain 'A' and resid 655 through 682 Processing helix chain 'A' and resid 689 through 712 removed outlier: 5.869A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 62 Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.629A pdb=" N LYS B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 99 through 125 Processing helix chain 'B' and resid 129 through 143 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 164 through 194 removed outlier: 3.900A pdb=" N TYR B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 174 - end of helix Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 204 through 216 Processing helix chain 'B' and resid 217 through 234 Processing helix chain 'B' and resid 238 through 265 removed outlier: 3.670A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'B' and resid 326 through 336 removed outlier: 4.120A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 367 removed outlier: 3.617A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 411 through 436 removed outlier: 3.577A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 473 Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.992A pdb=" N ILE B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix removed outlier: 3.728A pdb=" N VAL B 496 " --> pdb=" O PRO B 492 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 543 Processing helix chain 'B' and resid 655 through 682 Processing helix chain 'B' and resid 689 through 712 removed outlier: 5.870A pdb=" N GLY B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2142 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: 2.50 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1250 1.32 - 1.44: 2387 1.44 - 1.57: 5067 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 8794 Sorted by residual: bond pdb=" CD1 TYR A 320 " pdb=" CE1 TYR A 320 " ideal model delta sigma weight residual 1.382 1.337 0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" CD1 TYR B 320 " pdb=" CE1 TYR B 320 " ideal model delta sigma weight residual 1.382 1.338 0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CB TYR A 320 " pdb=" CG TYR A 320 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.20e-02 2.07e+03 2.02e+00 bond pdb=" C LEU B 665 " pdb=" O LEU B 665 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.19e-02 7.06e+03 2.01e+00 bond pdb=" C SER B 251 " pdb=" O SER B 251 " ideal model delta sigma weight residual 1.236 1.253 -0.018 1.29e-02 6.01e+03 1.92e+00 ... (remaining 8789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11371 2.02 - 4.04: 484 4.04 - 6.05: 75 6.05 - 8.07: 8 8.07 - 10.09: 4 Bond angle restraints: 11942 Sorted by residual: angle pdb=" C GLU A 242 " pdb=" N ASN A 243 " pdb=" CA ASN A 243 " ideal model delta sigma weight residual 121.58 111.49 10.09 1.95e+00 2.63e-01 2.68e+01 angle pdb=" C GLU B 242 " pdb=" N ASN B 243 " pdb=" CA ASN B 243 " ideal model delta sigma weight residual 121.58 111.49 10.09 1.95e+00 2.63e-01 2.68e+01 angle pdb=" C VAL A 698 " pdb=" N PHE A 699 " pdb=" CA PHE A 699 " ideal model delta sigma weight residual 120.44 115.63 4.81 1.36e+00 5.41e-01 1.25e+01 angle pdb=" CA PHE A 221 " pdb=" CB PHE A 221 " pdb=" CG PHE A 221 " ideal model delta sigma weight residual 113.80 117.32 -3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" CA PHE B 221 " pdb=" CB PHE B 221 " pdb=" CG PHE B 221 " ideal model delta sigma weight residual 113.80 117.32 -3.52 1.00e+00 1.00e+00 1.24e+01 ... (remaining 11937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.86: 5020 23.86 - 47.73: 156 47.73 - 71.59: 30 71.59 - 95.45: 2 95.45 - 119.31: 6 Dihedral angle restraints: 5214 sinusoidal: 2076 harmonic: 3138 Sorted by residual: dihedral pdb=" CA GLN A 143 " pdb=" C GLN A 143 " pdb=" N SER A 144 " pdb=" CA SER A 144 " ideal model delta harmonic sigma weight residual -180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA GLN B 143 " pdb=" C GLN B 143 " pdb=" N SER B 144 " pdb=" CA SER B 144 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA TYR B 516 " pdb=" C TYR B 516 " pdb=" N GLY B 517 " pdb=" CA GLY B 517 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 5211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1048 0.052 - 0.103: 314 0.103 - 0.155: 74 0.155 - 0.206: 4 0.206 - 0.258: 8 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ASN A 243 " pdb=" N ASN A 243 " pdb=" C ASN A 243 " pdb=" CB ASN A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL B 425 " pdb=" CA VAL B 425 " pdb=" CG1 VAL B 425 " pdb=" CG2 VAL B 425 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1445 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 320 " 0.056 2.00e-02 2.50e+03 2.89e-02 1.67e+01 pdb=" CG TYR B 320 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 320 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 320 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 320 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 320 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 320 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.056 2.00e-02 2.50e+03 2.85e-02 1.63e+01 pdb=" CG TYR A 320 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 221 " 0.029 2.00e-02 2.50e+03 2.24e-02 8.75e+00 pdb=" CG PHE B 221 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 221 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 221 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 221 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 221 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 221 " 0.005 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3367 2.90 - 3.40: 9559 3.40 - 3.90: 15526 3.90 - 4.40: 17942 4.40 - 4.90: 29501 Nonbonded interactions: 75895 Sorted by model distance: nonbonded pdb=" CG1 VAL B 348 " pdb=" CBQ LMN B 901 " model vdw 2.398 3.860 nonbonded pdb=" CG1 VAL A 348 " pdb=" CBQ LMN A 901 " model vdw 2.399 3.860 nonbonded pdb=" CE MET A 264 " pdb=" CBL LMN A 901 " model vdw 2.448 3.860 nonbonded pdb=" CE MET B 264 " pdb=" CBL LMN B 901 " model vdw 2.449 3.860 nonbonded pdb=" O GLN B 520 " pdb=" OG1 THR B 524 " model vdw 2.476 3.040 ... (remaining 75890 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.210 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.090 Find NCS groups from input model: 0.150 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 0.049 8794 Z= 0.330 Angle : 0.963 10.090 11942 Z= 0.546 Chirality : 0.053 0.258 1448 Planarity : 0.008 0.072 1406 Dihedral : 13.549 119.315 3186 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: -0.73 (0.24), residues: 1058 helix: -0.39 (0.15), residues: 894 sheet: None (None), residues: 0 loop : 0.01 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP B 100 HIS 0.007 0.003 HIS B 310 PHE 0.050 0.005 PHE A 221 TYR 0.056 0.005 TYR B 320 ARG 0.004 0.001 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.10975 ( 722) hydrogen bonds : angle 6.41557 ( 2142) covalent geometry : bond 0.00707 ( 8794) covalent geometry : angle 0.96323 (11942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7773 (m-10) cc_final: 0.7428 (m-10) REVERT: A 246 ASP cc_start: 0.7917 (m-30) cc_final: 0.7551 (m-30) REVERT: A 347 MET cc_start: 0.8862 (tmm) cc_final: 0.8661 (tmm) REVERT: B 104 TYR cc_start: 0.7701 (m-10) cc_final: 0.7489 (m-10) REVERT: B 136 LEU cc_start: 0.8481 (mt) cc_final: 0.8112 (mt) REVERT: B 246 ASP cc_start: 0.7902 (m-30) cc_final: 0.7597 (m-30) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.9189 time to fit residues: 309.4402 Evaluate side-chains 167 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.0470 chunk 98 optimal weight: 0.0770 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 409 GLN A 672 ASN A 716 HIS B 310 HIS B 409 GLN B 716 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.137797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.111758 restraints weight = 15909.725| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.44 r_work: 0.3535 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8794 Z= 0.193 Angle : 0.754 7.879 11942 Z= 0.385 Chirality : 0.043 0.178 1448 Planarity : 0.005 0.040 1406 Dihedral : 6.951 79.406 1280 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 4.14 % Allowed : 14.01 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 1.64 (0.26), residues: 1058 helix: 1.21 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.91 (0.58), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 432 HIS 0.002 0.001 HIS A 412 PHE 0.032 0.002 PHE B 221 TYR 0.012 0.002 TYR A 168 ARG 0.006 0.001 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 722) hydrogen bonds : angle 5.32826 ( 2142) covalent geometry : bond 0.00430 ( 8794) covalent geometry : angle 0.75369 (11942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8276 (ptp-170) cc_final: 0.7694 (ptp-170) REVERT: A 179 MET cc_start: 0.8407 (mtm) cc_final: 0.7971 (mtm) REVERT: A 212 LEU cc_start: 0.8894 (tm) cc_final: 0.8575 (mt) REVERT: A 213 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8400 (mtp85) REVERT: A 295 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7998 (ttm-80) REVERT: A 296 GLU cc_start: 0.8789 (tp30) cc_final: 0.8338 (tp30) REVERT: A 352 PHE cc_start: 0.8375 (t80) cc_final: 0.7936 (t80) REVERT: A 396 TRP cc_start: 0.7640 (t60) cc_final: 0.7213 (t60) REVERT: A 413 MET cc_start: 0.8301 (ptm) cc_final: 0.7858 (ttp) REVERT: A 417 ASN cc_start: 0.8821 (m-40) cc_final: 0.8218 (m110) REVERT: A 469 PHE cc_start: 0.8246 (t80) cc_final: 0.7793 (t80) REVERT: B 130 ARG cc_start: 0.8141 (ptp90) cc_final: 0.7755 (ptp-170) REVERT: B 179 MET cc_start: 0.8468 (mtm) cc_final: 0.8165 (mtm) REVERT: B 296 GLU cc_start: 0.8768 (tp30) cc_final: 0.8397 (tp30) REVERT: B 352 PHE cc_start: 0.8399 (t80) cc_final: 0.7972 (t80) REVERT: B 396 TRP cc_start: 0.7688 (t60) cc_final: 0.7350 (t60) REVERT: B 413 MET cc_start: 0.8308 (ptm) cc_final: 0.8009 (ttp) REVERT: B 417 ASN cc_start: 0.8762 (m-40) cc_final: 0.8241 (m110) REVERT: B 469 PHE cc_start: 0.8208 (t80) cc_final: 0.7466 (t80) outliers start: 39 outliers final: 2 residues processed: 238 average time/residue: 0.9733 time to fit residues: 250.0316 Evaluate side-chains 173 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.135825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109163 restraints weight = 16308.391| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.55 r_work: 0.3497 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8794 Z= 0.204 Angle : 0.743 10.478 11942 Z= 0.368 Chirality : 0.044 0.266 1448 Planarity : 0.005 0.035 1406 Dihedral : 6.484 71.857 1280 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.40 % Allowed : 19.43 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.15 (0.26), residues: 1058 helix: 1.60 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.83 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 363 HIS 0.002 0.001 HIS A 716 PHE 0.027 0.002 PHE A 384 TYR 0.012 0.002 TYR B 455 ARG 0.006 0.001 ARG B 657 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 722) hydrogen bonds : angle 5.15945 ( 2142) covalent geometry : bond 0.00477 ( 8794) covalent geometry : angle 0.74315 (11942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8287 (ptp-170) cc_final: 0.7957 (ptp-170) REVERT: A 413 MET cc_start: 0.8189 (ptm) cc_final: 0.7814 (ttp) REVERT: A 417 ASN cc_start: 0.8750 (m-40) cc_final: 0.8137 (m110) REVERT: A 420 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 430 MET cc_start: 0.7558 (mtp) cc_final: 0.7336 (mtp) REVERT: A 458 TYR cc_start: 0.7654 (m-10) cc_final: 0.7445 (m-80) REVERT: A 514 PHE cc_start: 0.7770 (m-80) cc_final: 0.7234 (m-80) REVERT: B 130 ARG cc_start: 0.8257 (ptp90) cc_final: 0.7857 (ptp-170) REVERT: B 212 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8428 (tm) REVERT: B 296 GLU cc_start: 0.8767 (tp30) cc_final: 0.8371 (tp30) REVERT: B 297 MET cc_start: 0.8563 (mmt) cc_final: 0.8305 (mpt) REVERT: B 413 MET cc_start: 0.8092 (ptm) cc_final: 0.7807 (ttp) REVERT: B 417 ASN cc_start: 0.8841 (m-40) cc_final: 0.8266 (m110) REVERT: B 430 MET cc_start: 0.7530 (mtp) cc_final: 0.7316 (mtp) REVERT: B 447 PHE cc_start: 0.8184 (t80) cc_final: 0.7978 (t80) REVERT: B 514 PHE cc_start: 0.7751 (m-80) cc_final: 0.7163 (m-80) outliers start: 32 outliers final: 10 residues processed: 210 average time/residue: 0.9588 time to fit residues: 217.9090 Evaluate side-chains 185 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.135153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.108626 restraints weight = 16196.888| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.55 r_work: 0.3489 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8794 Z= 0.203 Angle : 0.719 12.273 11942 Z= 0.361 Chirality : 0.044 0.270 1448 Planarity : 0.005 0.043 1406 Dihedral : 6.506 73.701 1280 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.25 % Allowed : 17.94 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.37 (0.26), residues: 1058 helix: 1.73 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 1.00 (0.56), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 363 HIS 0.001 0.001 HIS B 412 PHE 0.032 0.002 PHE A 221 TYR 0.012 0.001 TYR B 455 ARG 0.009 0.001 ARG B 657 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 722) hydrogen bonds : angle 5.08855 ( 2142) covalent geometry : bond 0.00478 ( 8794) covalent geometry : angle 0.71877 (11942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8393 (mtm-85) REVERT: A 130 ARG cc_start: 0.8283 (ptp-170) cc_final: 0.7936 (ptp-170) REVERT: A 155 GLU cc_start: 0.8998 (tt0) cc_final: 0.8245 (tt0) REVERT: A 159 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: A 212 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8956 (tm) REVERT: A 215 LEU cc_start: 0.9311 (mt) cc_final: 0.9067 (mm) REVERT: A 296 GLU cc_start: 0.8780 (tp30) cc_final: 0.8388 (tp30) REVERT: A 370 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6917 (mmm) REVERT: A 413 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7691 (ttp) REVERT: A 417 ASN cc_start: 0.8746 (m-40) cc_final: 0.8154 (m110) REVERT: A 420 ILE cc_start: 0.8899 (mp) cc_final: 0.8570 (tp) REVERT: A 469 PHE cc_start: 0.8227 (t80) cc_final: 0.7862 (t80) REVERT: B 41 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8463 (mtm-85) REVERT: B 130 ARG cc_start: 0.8287 (ptp90) cc_final: 0.7893 (ptp-170) REVERT: B 213 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8382 (ttt180) REVERT: B 296 GLU cc_start: 0.8766 (tp30) cc_final: 0.8377 (tp30) REVERT: B 413 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7700 (ttp) REVERT: B 414 LEU cc_start: 0.8408 (mt) cc_final: 0.8107 (mm) REVERT: B 417 ASN cc_start: 0.8832 (m-40) cc_final: 0.8205 (m110) REVERT: B 469 PHE cc_start: 0.8217 (t80) cc_final: 0.7817 (t80) outliers start: 40 outliers final: 8 residues processed: 197 average time/residue: 0.8786 time to fit residues: 187.8425 Evaluate side-chains 173 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 413 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.135631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.109322 restraints weight = 16271.042| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.54 r_work: 0.3497 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8794 Z= 0.193 Angle : 0.707 10.349 11942 Z= 0.356 Chirality : 0.044 0.269 1448 Planarity : 0.005 0.038 1406 Dihedral : 6.442 75.021 1280 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 4.03 % Allowed : 19.64 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.50 (0.26), residues: 1058 helix: 1.84 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.95 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 363 HIS 0.001 0.000 HIS B 658 PHE 0.032 0.002 PHE B 384 TYR 0.023 0.002 TYR A 458 ARG 0.008 0.001 ARG A 657 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 722) hydrogen bonds : angle 5.02347 ( 2142) covalent geometry : bond 0.00458 ( 8794) covalent geometry : angle 0.70732 (11942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8472 (mtm-85) REVERT: A 130 ARG cc_start: 0.8357 (ptp-170) cc_final: 0.8077 (ptp-170) REVERT: A 215 LEU cc_start: 0.9239 (mt) cc_final: 0.8994 (mm) REVERT: A 296 GLU cc_start: 0.8781 (tp30) cc_final: 0.8335 (tp30) REVERT: A 370 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6900 (mmm) REVERT: A 413 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7652 (ttp) REVERT: A 417 ASN cc_start: 0.8750 (m-40) cc_final: 0.8136 (m110) REVERT: A 430 MET cc_start: 0.7525 (mmm) cc_final: 0.7141 (mmm) REVERT: A 459 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8357 (mt) REVERT: A 469 PHE cc_start: 0.8240 (t80) cc_final: 0.7873 (t80) REVERT: A 657 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7589 (ttm110) REVERT: B 41 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8490 (mtm-85) REVERT: B 130 ARG cc_start: 0.8312 (ptp90) cc_final: 0.7969 (ptp-170) REVERT: B 370 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6874 (mmm) REVERT: B 413 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: B 417 ASN cc_start: 0.8793 (m-40) cc_final: 0.8232 (m110) REVERT: B 430 MET cc_start: 0.7605 (mmm) cc_final: 0.7213 (mmm) REVERT: B 459 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8278 (mt) REVERT: B 469 PHE cc_start: 0.8244 (t80) cc_final: 0.7884 (t80) REVERT: B 657 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7741 (ttm110) REVERT: B 691 GLU cc_start: 0.8719 (mp0) cc_final: 0.8504 (mp0) outliers start: 38 outliers final: 10 residues processed: 196 average time/residue: 0.9630 time to fit residues: 204.0646 Evaluate side-chains 172 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 0.0010 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.134485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.108286 restraints weight = 16139.108| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.52 r_work: 0.3485 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8794 Z= 0.222 Angle : 0.736 9.314 11942 Z= 0.371 Chirality : 0.044 0.255 1448 Planarity : 0.005 0.062 1406 Dihedral : 6.400 76.304 1280 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.25 % Allowed : 21.13 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.46 (0.26), residues: 1058 helix: 1.84 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.75 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 460 HIS 0.002 0.001 HIS A 412 PHE 0.028 0.002 PHE A 221 TYR 0.014 0.002 TYR A 451 ARG 0.009 0.001 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 722) hydrogen bonds : angle 5.06935 ( 2142) covalent geometry : bond 0.00532 ( 8794) covalent geometry : angle 0.73550 (11942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8360 (ptp-170) cc_final: 0.8053 (ptp-170) REVERT: A 213 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8420 (ptm-80) REVERT: A 296 GLU cc_start: 0.8753 (tp30) cc_final: 0.8311 (tp30) REVERT: A 370 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6848 (mmm) REVERT: A 413 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7662 (ttp) REVERT: A 417 ASN cc_start: 0.8681 (m-40) cc_final: 0.8023 (m110) REVERT: A 459 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 469 PHE cc_start: 0.8276 (t80) cc_final: 0.7948 (t80) REVERT: A 539 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 657 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7664 (ttm110) REVERT: B 130 ARG cc_start: 0.8325 (ptp90) cc_final: 0.7966 (ptp-170) REVERT: B 189 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8424 (mm-30) REVERT: B 296 GLU cc_start: 0.8716 (tp30) cc_final: 0.8358 (tp30) REVERT: B 370 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6936 (mmm) REVERT: B 413 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7702 (ttp) REVERT: B 417 ASN cc_start: 0.8794 (m-40) cc_final: 0.8226 (m110) REVERT: B 430 MET cc_start: 0.7558 (mmm) cc_final: 0.7326 (mmm) REVERT: B 459 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 657 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7699 (ttm110) REVERT: B 691 GLU cc_start: 0.8707 (mp0) cc_final: 0.8480 (mp0) outliers start: 40 outliers final: 13 residues processed: 188 average time/residue: 0.9489 time to fit residues: 193.0224 Evaluate side-chains 172 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 0.0470 chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 716 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.135886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109922 restraints weight = 16208.836| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.48 r_work: 0.3509 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8794 Z= 0.190 Angle : 0.735 9.029 11942 Z= 0.368 Chirality : 0.044 0.252 1448 Planarity : 0.004 0.028 1406 Dihedral : 6.396 76.019 1280 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.50 % Allowed : 22.72 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.51 (0.26), residues: 1058 helix: 1.87 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.78 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 460 HIS 0.001 0.001 HIS B 412 PHE 0.032 0.002 PHE A 384 TYR 0.014 0.002 TYR B 455 ARG 0.005 0.001 ARG B 657 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 722) hydrogen bonds : angle 5.02300 ( 2142) covalent geometry : bond 0.00452 ( 8794) covalent geometry : angle 0.73494 (11942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8352 (ptp-170) cc_final: 0.8089 (ptp-170) REVERT: A 296 GLU cc_start: 0.8673 (tp30) cc_final: 0.8255 (tp30) REVERT: A 370 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6882 (mmm) REVERT: A 373 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8729 (tppt) REVERT: A 413 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7659 (ttp) REVERT: A 417 ASN cc_start: 0.8668 (m-40) cc_final: 0.8024 (m110) REVERT: A 430 MET cc_start: 0.7606 (mmm) cc_final: 0.7367 (mpp) REVERT: A 459 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8427 (mt) REVERT: A 469 PHE cc_start: 0.8254 (t80) cc_final: 0.7931 (t80) REVERT: B 130 ARG cc_start: 0.8314 (ptp90) cc_final: 0.8004 (ptp-170) REVERT: B 296 GLU cc_start: 0.8664 (tp30) cc_final: 0.8326 (tp30) REVERT: B 370 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6883 (mmm) REVERT: B 417 ASN cc_start: 0.8804 (m-40) cc_final: 0.8305 (m110) REVERT: B 459 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 469 PHE cc_start: 0.8252 (t80) cc_final: 0.7911 (t80) REVERT: B 657 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7747 (ttm110) REVERT: B 691 GLU cc_start: 0.8655 (mp0) cc_final: 0.8430 (mp0) REVERT: B 714 ASP cc_start: 0.7793 (t0) cc_final: 0.7192 (t0) outliers start: 33 outliers final: 12 residues processed: 186 average time/residue: 0.9946 time to fit residues: 200.0411 Evaluate side-chains 172 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 80 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.136007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109807 restraints weight = 16390.588| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.53 r_work: 0.3509 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8794 Z= 0.195 Angle : 0.748 8.899 11942 Z= 0.376 Chirality : 0.044 0.254 1448 Planarity : 0.004 0.047 1406 Dihedral : 6.361 76.878 1280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.61 % Allowed : 23.04 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.51 (0.26), residues: 1058 helix: 1.88 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.71 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.004 0.001 HIS B 716 PHE 0.029 0.002 PHE A 384 TYR 0.022 0.002 TYR A 451 ARG 0.007 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04847 ( 722) hydrogen bonds : angle 5.02971 ( 2142) covalent geometry : bond 0.00467 ( 8794) covalent geometry : angle 0.74774 (11942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8319 (ptp-170) cc_final: 0.8037 (ptp-170) REVERT: A 213 ARG cc_start: 0.8674 (ptm-80) cc_final: 0.8248 (ptm-80) REVERT: A 296 GLU cc_start: 0.8699 (tp30) cc_final: 0.8262 (tp30) REVERT: A 373 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8791 (tppt) REVERT: A 417 ASN cc_start: 0.8649 (m-40) cc_final: 0.8062 (m110) REVERT: A 459 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8422 (mt) REVERT: A 469 PHE cc_start: 0.8278 (t80) cc_final: 0.7931 (t80) REVERT: A 539 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7923 (mp) REVERT: B 130 ARG cc_start: 0.8314 (ptp90) cc_final: 0.8030 (ptp-170) REVERT: B 296 GLU cc_start: 0.8710 (tp30) cc_final: 0.8350 (tp30) REVERT: B 370 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6741 (mmm) REVERT: B 417 ASN cc_start: 0.8791 (m-40) cc_final: 0.8298 (m110) REVERT: B 430 MET cc_start: 0.7469 (mpp) cc_final: 0.7248 (mpp) REVERT: B 459 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8442 (mt) REVERT: B 469 PHE cc_start: 0.8285 (t80) cc_final: 0.7910 (t80) REVERT: B 657 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7625 (ttm110) REVERT: B 691 GLU cc_start: 0.8696 (mp0) cc_final: 0.8458 (mp0) REVERT: B 716 HIS cc_start: 0.6241 (m-70) cc_final: 0.5797 (m90) outliers start: 34 outliers final: 13 residues processed: 192 average time/residue: 0.9382 time to fit residues: 194.9223 Evaluate side-chains 178 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.136876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110650 restraints weight = 16252.131| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.53 r_work: 0.3523 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8794 Z= 0.187 Angle : 0.747 8.437 11942 Z= 0.375 Chirality : 0.044 0.259 1448 Planarity : 0.004 0.028 1406 Dihedral : 6.392 77.357 1280 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.65 % Allowed : 24.20 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.56 (0.26), residues: 1058 helix: 1.90 (0.17), residues: 894 sheet: None (None), residues: 0 loop : 0.79 (0.56), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 460 HIS 0.003 0.001 HIS B 716 PHE 0.029 0.002 PHE B 701 TYR 0.014 0.002 TYR B 455 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 722) hydrogen bonds : angle 5.02359 ( 2142) covalent geometry : bond 0.00446 ( 8794) covalent geometry : angle 0.74731 (11942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8320 (ptp-170) cc_final: 0.8058 (ptp-170) REVERT: A 213 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8374 (ptm-80) REVERT: A 373 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8778 (tptt) REVERT: A 417 ASN cc_start: 0.8669 (m-40) cc_final: 0.8099 (m110) REVERT: A 429 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.6569 (tmm) REVERT: A 459 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8424 (mt) REVERT: A 469 PHE cc_start: 0.8252 (t80) cc_final: 0.7916 (t80) REVERT: A 539 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 714 ASP cc_start: 0.7818 (t0) cc_final: 0.7202 (t0) REVERT: A 716 HIS cc_start: 0.6663 (m-70) cc_final: 0.6047 (m90) REVERT: B 130 ARG cc_start: 0.8306 (ptp90) cc_final: 0.8023 (ptp-170) REVERT: B 213 ARG cc_start: 0.8760 (ptm-80) cc_final: 0.8418 (ptm-80) REVERT: B 296 GLU cc_start: 0.8726 (tp30) cc_final: 0.8366 (tp30) REVERT: B 370 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6767 (mmm) REVERT: B 417 ASN cc_start: 0.8771 (m-40) cc_final: 0.8225 (m110) REVERT: B 455 TYR cc_start: 0.7740 (m-80) cc_final: 0.7393 (m-80) REVERT: B 458 TYR cc_start: 0.7586 (m-10) cc_final: 0.6904 (m-10) REVERT: B 459 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 469 PHE cc_start: 0.8281 (t80) cc_final: 0.7881 (t80) REVERT: B 657 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7630 (ttm110) outliers start: 25 outliers final: 15 residues processed: 187 average time/residue: 0.9619 time to fit residues: 194.3694 Evaluate side-chains 178 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 0.0470 chunk 70 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.137027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.110624 restraints weight = 16153.795| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.53 r_work: 0.3523 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8794 Z= 0.198 Angle : 0.788 8.884 11942 Z= 0.396 Chirality : 0.044 0.225 1448 Planarity : 0.004 0.030 1406 Dihedral : 6.358 77.473 1280 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.55 % Allowed : 25.05 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.52 (0.26), residues: 1058 helix: 1.88 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 0.73 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 100 HIS 0.002 0.001 HIS B 716 PHE 0.041 0.002 PHE A 701 TYR 0.029 0.002 TYR A 451 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 722) hydrogen bonds : angle 5.03362 ( 2142) covalent geometry : bond 0.00480 ( 8794) covalent geometry : angle 0.78830 (11942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8312 (ptp-170) cc_final: 0.8043 (ptp-170) REVERT: A 417 ASN cc_start: 0.8662 (m-40) cc_final: 0.8077 (m110) REVERT: A 429 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.6326 (tmm) REVERT: A 459 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 469 PHE cc_start: 0.8249 (t80) cc_final: 0.7922 (t80) REVERT: A 539 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7703 (mp) REVERT: A 714 ASP cc_start: 0.7784 (t0) cc_final: 0.7210 (t0) REVERT: A 716 HIS cc_start: 0.6483 (m-70) cc_final: 0.6003 (m90) REVERT: B 130 ARG cc_start: 0.8300 (ptp90) cc_final: 0.7994 (ptp-170) REVERT: B 159 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: B 296 GLU cc_start: 0.8709 (tp30) cc_final: 0.8333 (tp30) REVERT: B 370 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6820 (mmm) REVERT: B 417 ASN cc_start: 0.8734 (m-40) cc_final: 0.8188 (m110) REVERT: B 429 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.6577 (tmm) REVERT: B 455 TYR cc_start: 0.7747 (m-80) cc_final: 0.7417 (m-80) REVERT: B 458 TYR cc_start: 0.7598 (m-10) cc_final: 0.6876 (m-10) REVERT: B 459 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8387 (mt) REVERT: B 469 PHE cc_start: 0.8212 (t80) cc_final: 0.7819 (t80) REVERT: B 657 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7629 (ttm110) outliers start: 24 outliers final: 11 residues processed: 185 average time/residue: 0.9965 time to fit residues: 198.9879 Evaluate side-chains 183 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 12 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS B 337 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.137178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.110893 restraints weight = 16222.921| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.53 r_work: 0.3527 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8794 Z= 0.195 Angle : 0.795 8.741 11942 Z= 0.400 Chirality : 0.045 0.267 1448 Planarity : 0.005 0.067 1406 Dihedral : 6.377 76.591 1280 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.55 % Allowed : 25.48 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 2.46 (0.26), residues: 1058 helix: 1.84 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 0.72 (0.55), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 100 HIS 0.002 0.001 HIS B 716 PHE 0.042 0.002 PHE B 701 TYR 0.015 0.002 TYR B 455 ARG 0.009 0.001 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 722) hydrogen bonds : angle 5.05284 ( 2142) covalent geometry : bond 0.00477 ( 8794) covalent geometry : angle 0.79457 (11942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6371.03 seconds wall clock time: 110 minutes 5.52 seconds (6605.52 seconds total)