Starting phenix.real_space_refine on Fri Nov 15 07:59:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u56_41913/11_2024/8u56_41913.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u56_41913/11_2024/8u56_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u56_41913/11_2024/8u56_41913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u56_41913/11_2024/8u56_41913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u56_41913/11_2024/8u56_41913.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u56_41913/11_2024/8u56_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-5513/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: 7.81, per 1000 atoms: 0.91 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: 2.72 Conformation dependent library (CDL) restraints added in 1.1 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: 0.80 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: 2.63 Time building geometry restraints manager: 3.02 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: 0.00 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: 0.940 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.470 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- 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= 0.454 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 *********************** 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 : 1.019 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: 0.9479 time to fit residues: 319.1894 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 : 0.985 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8794 Z= 0.278 Angle : 0.755 7.920 11942 Z= 0.385 Chirality : 0.043 0.177 1448 Planarity : 0.005 0.040 1406 Dihedral : 7.024 79.260 1280 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.18 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: 1.63 (0.26), residues: 1058 helix: 1.20 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.92 (0.58), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 *********************** 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 256 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7736 (m-10) cc_final: 0.7510 (m-10) REVERT: A 246 ASP cc_start: 0.7896 (m-30) cc_final: 0.7576 (m-30) REVERT: A 296 GLU cc_start: 0.8089 (tp30) cc_final: 0.7825 (tp30) REVERT: A 396 TRP cc_start: 0.7435 (t60) cc_final: 0.7227 (t60) REVERT: A 534 ILE cc_start: 0.7934 (mt) cc_final: 0.7708 (pt) REVERT: B 246 ASP cc_start: 0.7882 (m-30) cc_final: 0.7557 (m-30) REVERT: B 296 GLU cc_start: 0.8070 (tp30) cc_final: 0.7816 (tp30) REVERT: B 469 PHE cc_start: 0.7555 (t80) cc_final: 0.7340 (t80) REVERT: B 534 ILE cc_start: 0.7941 (mt) cc_final: 0.7733 (pt) outliers start: 39 outliers final: 2 residues processed: 237 average time/residue: 0.9789 time to fit residues: 250.4518 Evaluate side-chains 178 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.0770 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 716 HIS B 409 GLN B 716 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8794 Z= 0.273 Angle : 0.739 10.820 11942 Z= 0.366 Chirality : 0.044 0.271 1448 Planarity : 0.005 0.035 1406 Dihedral : 6.660 80.606 1280 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.72 % Allowed : 18.90 % Favored : 77.39 % 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: 2.24 (0.26), residues: 1058 helix: 1.67 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.82 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 489 HIS 0.001 0.000 HIS A 716 PHE 0.028 0.002 PHE A 384 TYR 0.013 0.002 TYR B 455 ARG 0.007 0.001 ARG A 474 *********************** 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 228 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.5864 (mp10) REVERT: A 514 PHE cc_start: 0.6487 (m-80) cc_final: 0.6143 (m-80) REVERT: A 534 ILE cc_start: 0.8262 (mt) cc_final: 0.7908 (pt) REVERT: B 246 ASP cc_start: 0.7914 (m-30) cc_final: 0.7646 (m-30) REVERT: B 296 GLU cc_start: 0.8068 (tp30) cc_final: 0.7805 (tp30) REVERT: B 409 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6107 (mp10) REVERT: B 514 PHE cc_start: 0.6574 (m-80) cc_final: 0.6207 (m-80) REVERT: B 534 ILE cc_start: 0.8293 (mt) cc_final: 0.7901 (pt) outliers start: 35 outliers final: 6 residues processed: 212 average time/residue: 0.9640 time to fit residues: 220.9230 Evaluate side-chains 177 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 409 GLN 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 409 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN B 409 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8794 Z= 0.361 Angle : 0.750 9.309 11942 Z= 0.374 Chirality : 0.045 0.310 1448 Planarity : 0.005 0.034 1406 Dihedral : 6.663 74.878 1280 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.14 % Allowed : 17.94 % Favored : 77.92 % 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: 2.34 (0.26), residues: 1058 helix: 1.76 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 0.67 (0.55), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 363 HIS 0.002 0.001 HIS B 716 PHE 0.031 0.002 PHE B 221 TYR 0.021 0.002 TYR A 458 ARG 0.009 0.001 ARG B 657 *********************** 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 211 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7387 (mtm-85) REVERT: A 242 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7720 (tm-30) REVERT: A 296 GLU cc_start: 0.8024 (tp30) cc_final: 0.7771 (tp30) REVERT: A 370 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7197 (mmt) REVERT: A 459 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8164 (mt) REVERT: A 521 MET cc_start: 0.5927 (tpt) cc_final: 0.5681 (tpt) REVERT: A 534 ILE cc_start: 0.8308 (mt) cc_final: 0.7975 (pt) REVERT: B 37 MET cc_start: 0.4885 (OUTLIER) cc_final: 0.4230 (tmm) REVERT: B 159 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: B 242 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 370 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7269 (mmt) REVERT: B 430 MET cc_start: 0.7136 (mtp) cc_final: 0.6820 (mtt) REVERT: B 534 ILE cc_start: 0.8282 (mt) cc_final: 0.7958 (pt) outliers start: 39 outliers final: 9 residues processed: 198 average time/residue: 0.9328 time to fit residues: 199.8142 Evaluate side-chains 175 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 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 459 LEU Chi-restraints excluded: chain B residue 37 MET 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 179 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8794 Z= 0.295 Angle : 0.723 8.012 11942 Z= 0.361 Chirality : 0.044 0.266 1448 Planarity : 0.004 0.029 1406 Dihedral : 6.647 76.686 1280 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.82 % Allowed : 20.06 % Favored : 76.11 % 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: 892 sheet: None (None), residues: 0 loop : 0.76 (0.57), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 460 HIS 0.001 0.001 HIS B 412 PHE 0.028 0.002 PHE B 221 TYR 0.016 0.002 TYR B 451 ARG 0.007 0.001 ARG B 657 *********************** 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 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.7914 (mtm) cc_final: 0.7652 (ptm) REVERT: A 212 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7931 (mm) REVERT: A 246 ASP cc_start: 0.7730 (m-30) cc_final: 0.7293 (m-30) REVERT: A 296 GLU cc_start: 0.7979 (tp30) cc_final: 0.7713 (tp30) REVERT: A 370 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7800 (mmm) REVERT: A 521 MET cc_start: 0.5829 (tpt) cc_final: 0.5612 (tpt) REVERT: A 534 ILE cc_start: 0.8302 (mt) cc_final: 0.7961 (pt) REVERT: B 246 ASP cc_start: 0.7759 (m-30) cc_final: 0.7400 (m-30) REVERT: B 296 GLU cc_start: 0.7967 (tp30) cc_final: 0.7746 (tp30) REVERT: B 370 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7817 (mmm) REVERT: B 459 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8205 (mt) REVERT: B 469 PHE cc_start: 0.7389 (t80) cc_final: 0.7159 (t80) REVERT: B 534 ILE cc_start: 0.8296 (mt) cc_final: 0.8012 (pt) outliers start: 36 outliers final: 7 residues processed: 199 average time/residue: 0.9319 time to fit residues: 201.1682 Evaluate side-chains 170 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 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 B residue 136 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 416 THR 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 35 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8794 Z= 0.273 Angle : 0.724 9.387 11942 Z= 0.364 Chirality : 0.044 0.231 1448 Planarity : 0.005 0.046 1406 Dihedral : 6.591 77.083 1280 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.72 % Allowed : 21.76 % Favored : 74.52 % 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: 2.58 (0.26), residues: 1058 helix: 1.95 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 0.60 (0.57), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 460 HIS 0.002 0.001 HIS A 658 PHE 0.026 0.002 PHE B 221 TYR 0.016 0.002 TYR B 359 ARG 0.014 0.001 ARG B 41 *********************** 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 219 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7856 (mm) REVERT: A 534 ILE cc_start: 0.8287 (mt) cc_final: 0.7959 (pt) REVERT: B 296 GLU cc_start: 0.7969 (tp30) cc_final: 0.7745 (tp30) REVERT: B 370 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7801 (mmm) REVERT: B 469 PHE cc_start: 0.7318 (t80) cc_final: 0.7110 (t80) REVERT: B 484 ILE cc_start: 0.8044 (mm) cc_final: 0.7788 (tp) REVERT: B 534 ILE cc_start: 0.8289 (mt) cc_final: 0.8017 (pt) outliers start: 35 outliers final: 12 residues processed: 206 average time/residue: 1.0564 time to fit residues: 236.1298 Evaluate side-chains 177 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 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 416 THR Chi-restraints excluded: chain A residue 420 ILE 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 409 GLN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.0170 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 520 GLN A 716 HIS B 337 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8794 Z= 0.267 Angle : 0.735 8.327 11942 Z= 0.370 Chirality : 0.044 0.224 1448 Planarity : 0.004 0.046 1406 Dihedral : 6.541 78.283 1280 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.61 % Allowed : 22.82 % Favored : 73.57 % 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: 2.66 (0.26), residues: 1058 helix: 2.01 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.65 (0.55), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 460 HIS 0.002 0.001 HIS B 658 PHE 0.036 0.002 PHE A 384 TYR 0.015 0.002 TYR A 359 ARG 0.007 0.001 ARG A 235 *********************** 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 219 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7677 (mmm) REVERT: A 459 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8225 (mt) REVERT: A 534 ILE cc_start: 0.8273 (mt) cc_final: 0.7987 (pt) REVERT: A 539 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8256 (mp) REVERT: B 296 GLU cc_start: 0.7899 (tp30) cc_final: 0.7689 (tp30) REVERT: B 370 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7803 (mmm) REVERT: B 458 TYR cc_start: 0.7923 (m-10) cc_final: 0.6982 (m-10) REVERT: B 459 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8237 (mt) REVERT: B 469 PHE cc_start: 0.7364 (t80) cc_final: 0.7149 (t80) REVERT: B 484 ILE cc_start: 0.8028 (mm) cc_final: 0.7820 (tp) REVERT: B 534 ILE cc_start: 0.8283 (mt) cc_final: 0.8019 (pt) REVERT: B 714 ASP cc_start: 0.7371 (t0) cc_final: 0.7171 (t0) outliers start: 34 outliers final: 9 residues processed: 202 average time/residue: 0.9277 time to fit residues: 203.5145 Evaluate side-chains 177 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 539 LEU 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 409 GLN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8794 Z= 0.264 Angle : 0.760 9.731 11942 Z= 0.381 Chirality : 0.044 0.237 1448 Planarity : 0.004 0.028 1406 Dihedral : 6.470 78.458 1280 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.76 % Allowed : 24.95 % Favored : 72.29 % 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: 2.64 (0.26), residues: 1058 helix: 1.97 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 0.71 (0.55), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 460 HIS 0.004 0.001 HIS B 716 PHE 0.033 0.002 PHE A 384 TYR 0.017 0.002 TYR B 451 ARG 0.005 0.001 ARG B 657 *********************** 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 206 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 429 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.6841 (tmm) REVERT: A 459 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 534 ILE cc_start: 0.8193 (mt) cc_final: 0.7924 (pt) REVERT: B 213 ARG cc_start: 0.7783 (ptm-80) cc_final: 0.6946 (ptm-80) REVERT: B 296 GLU cc_start: 0.7871 (tp30) cc_final: 0.7662 (tp30) REVERT: B 458 TYR cc_start: 0.7841 (m-10) cc_final: 0.6965 (m-10) REVERT: B 459 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8160 (mt) REVERT: B 534 ILE cc_start: 0.8200 (mt) cc_final: 0.7947 (pt) REVERT: B 539 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8065 (mp) outliers start: 26 outliers final: 9 residues processed: 196 average time/residue: 0.9311 time to fit residues: 198.0062 Evaluate side-chains 177 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 539 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8794 Z= 0.300 Angle : 0.777 9.130 11942 Z= 0.393 Chirality : 0.045 0.225 1448 Planarity : 0.004 0.028 1406 Dihedral : 6.481 80.644 1280 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.97 % Allowed : 25.48 % Favored : 71.55 % 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: 1.93 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.49 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 460 HIS 0.003 0.001 HIS B 716 PHE 0.034 0.002 PHE A 701 TYR 0.022 0.002 TYR A 377 ARG 0.005 0.001 ARG B 657 *********************** 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 190 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 296 GLU cc_start: 0.8008 (tp30) cc_final: 0.7747 (tp30) REVERT: A 370 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7738 (mmm) REVERT: A 459 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8258 (mt) REVERT: A 534 ILE cc_start: 0.8283 (mt) cc_final: 0.8017 (pt) REVERT: A 714 ASP cc_start: 0.7325 (t0) cc_final: 0.7037 (t0) REVERT: B 296 GLU cc_start: 0.7929 (tp30) cc_final: 0.7721 (tp30) REVERT: B 429 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.6655 (tmm) REVERT: B 458 TYR cc_start: 0.7897 (m-10) cc_final: 0.6966 (m-10) REVERT: B 459 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8203 (mt) REVERT: B 534 ILE cc_start: 0.8297 (mt) cc_final: 0.8033 (pt) outliers start: 28 outliers final: 12 residues processed: 181 average time/residue: 0.9413 time to fit residues: 184.8181 Evaluate side-chains 178 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 416 THR 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 171 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 420 ILE 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 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 0.0030 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 337 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5366 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= 0.266 Angle : 0.793 10.887 11942 Z= 0.401 Chirality : 0.045 0.253 1448 Planarity : 0.004 0.030 1406 Dihedral : 6.544 81.411 1280 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.12 % Allowed : 27.07 % Favored : 70.81 % 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: 2.48 (0.25), residues: 1058 helix: 1.90 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.49 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 460 HIS 0.005 0.001 HIS A 716 PHE 0.030 0.002 PHE A 384 TYR 0.018 0.001 TYR B 451 ARG 0.006 0.001 ARG B 235 ********************** 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: 20 poor density : 177 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8276 (mt) REVERT: A 534 ILE cc_start: 0.8211 (mt) cc_final: 0.7985 (pt) REVERT: B 458 TYR cc_start: 0.7825 (m-10) cc_final: 0.6870 (m-10) REVERT: B 534 ILE cc_start: 0.8203 (mt) cc_final: 0.7970 (pt) outliers start: 20 outliers final: 8 residues processed: 185 average time/residue: 0.9733 time to fit residues: 194.8396 Evaluate side-chains 176 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 459 LEU 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 388 ILE Chi-restraints excluded: chain B residue 409 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN B 700 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.138727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111729 restraints weight = 15877.654| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.56 r_work: 0.3535 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8794 Z= 0.323 Angle : 0.822 10.490 11942 Z= 0.414 Chirality : 0.046 0.249 1448 Planarity : 0.004 0.033 1406 Dihedral : 6.539 82.104 1280 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.44 % Allowed : 26.43 % Favored : 71.13 % 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: 2.32 (0.25), residues: 1058 helix: 1.78 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.47 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 460 HIS 0.006 0.001 HIS A 716 PHE 0.029 0.002 PHE B 447 TYR 0.021 0.002 TYR A 377 ARG 0.006 0.001 ARG B 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.25 seconds wall clock time: 68 minutes 9.79 seconds (4089.79 seconds total)