Starting phenix.real_space_refine on Fri Nov 15 00:33:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpd_16779/11_2024/8cpd_16779.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpd_16779/11_2024/8cpd_16779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpd_16779/11_2024/8cpd_16779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpd_16779/11_2024/8cpd_16779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpd_16779/11_2024/8cpd_16779.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpd_16779/11_2024/8cpd_16779.cif" } resolution = 3.46 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 44 5.16 5 C 5096 2.51 5 N 1374 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 8030 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2173 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1842 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2173 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain breaks: 2 Chain: "D" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1842 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.67 Number of scatterers: 8030 At special positions: 0 Unit cell: (85.527, 91.375, 97.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 2 15.00 O 1514 8.00 N 1374 7.00 C 5096 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: 1.68 Conformation dependent library (CDL) restraints added in 1.6 seconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 4 sheets defined 62.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 383 through 398 Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.607A pdb=" N HIS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 removed outlier: 4.156A pdb=" N ASP A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 526 through 544 removed outlier: 4.151A pdb=" N ASP A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.645A pdb=" N LYS A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 613 Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 21 through 35 removed outlier: 3.841A pdb=" N MET C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 71 removed outlier: 3.981A pdb=" N LYS C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 110 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 117 through 137 Processing helix chain 'C' and resid 141 through 165 Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 190 through 208 removed outlier: 3.695A pdb=" N ALA C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 236 removed outlier: 4.210A pdb=" N LEU C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.777A pdb=" N LYS B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.593A pdb=" N HIS B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 462 removed outlier: 4.139A pdb=" N ASP B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 526 through 544 removed outlier: 4.119A pdb=" N ASP B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 563 Processing helix chain 'B' and resid 578 through 589 removed outlier: 3.518A pdb=" N LYS B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'D' and resid 5 through 19 Processing helix chain 'D' and resid 21 through 36 removed outlier: 3.824A pdb=" N MET D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 71 removed outlier: 3.996A pdb=" N LYS D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 110 Processing helix chain 'D' and resid 117 through 137 Processing helix chain 'D' and resid 141 through 165 Processing helix chain 'D' and resid 170 through 187 Processing helix chain 'D' and resid 190 through 208 removed outlier: 3.678A pdb=" N ALA D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 236 removed outlier: 4.210A pdb=" N LEU D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 353 removed outlier: 5.525A pdb=" N LEU A 351 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 367 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 419 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AA3, first strand: chain 'B' and resid 350 through 353 removed outlier: 5.530A pdb=" N LEU B 351 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS B 367 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 419 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN B 422 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE B 408 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 474 through 477 492 hydrogen bonds defined for protein. 1458 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: 2.25 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2358 1.34 - 1.46: 1272 1.46 - 1.58: 4459 1.58 - 1.70: 9 1.70 - 1.82: 78 Bond restraints: 8176 Sorted by residual: bond pdb=" C ALA D 154 " pdb=" N TYR D 155 " ideal model delta sigma weight residual 1.334 1.225 0.110 1.27e-02 6.20e+03 7.48e+01 bond pdb=" C TYR D 155 " pdb=" N GLN D 156 " ideal model delta sigma weight residual 1.335 1.435 -0.100 1.30e-02 5.92e+03 5.92e+01 bond pdb=" C LEU B 429 " pdb=" N TYR B 430 " ideal model delta sigma weight residual 1.334 1.263 0.072 1.43e-02 4.89e+03 2.51e+01 bond pdb=" C TYR B 430 " pdb=" N LYS B 431 " ideal model delta sigma weight residual 1.334 1.396 -0.062 1.27e-02 6.20e+03 2.35e+01 bond pdb=" C TYR A 430 " pdb=" N LYS A 431 " ideal model delta sigma weight residual 1.334 1.383 -0.049 1.27e-02 6.20e+03 1.49e+01 ... (remaining 8171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 10803 2.58 - 5.16: 190 5.16 - 7.75: 30 7.75 - 10.33: 1 10.33 - 12.91: 2 Bond angle restraints: 11026 Sorted by residual: angle pdb=" O ALA D 154 " pdb=" C ALA D 154 " pdb=" N TYR D 155 " ideal model delta sigma weight residual 122.07 114.92 7.15 1.03e+00 9.43e-01 4.82e+01 angle pdb=" CA ALA D 154 " pdb=" C ALA D 154 " pdb=" N TYR D 155 " ideal model delta sigma weight residual 117.07 124.02 -6.95 1.14e+00 7.69e-01 3.72e+01 angle pdb=" CA PRO D 168 " pdb=" N PRO D 168 " pdb=" CD PRO D 168 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" N TYR A 430 " pdb=" CA TYR A 430 " pdb=" C TYR A 430 " ideal model delta sigma weight residual 111.69 105.72 5.97 1.23e+00 6.61e-01 2.36e+01 angle pdb=" N TYR B 430 " pdb=" CA TYR B 430 " pdb=" C TYR B 430 " ideal model delta sigma weight residual 111.69 105.82 5.87 1.23e+00 6.61e-01 2.28e+01 ... (remaining 11021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4222 17.94 - 35.88: 641 35.88 - 53.82: 128 53.82 - 71.76: 13 71.76 - 89.70: 8 Dihedral angle restraints: 5012 sinusoidal: 2076 harmonic: 2936 Sorted by residual: dihedral pdb=" CA MET B 512 " pdb=" C MET B 512 " pdb=" N ALA B 513 " pdb=" CA ALA B 513 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA MET A 512 " pdb=" C MET A 512 " pdb=" N ALA A 513 " pdb=" CA ALA A 513 " ideal model delta harmonic sigma weight residual -180.00 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LYS C 165 " pdb=" C LYS C 165 " pdb=" N MET C 166 " pdb=" CA MET C 166 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 896 0.041 - 0.083: 237 0.083 - 0.124: 75 0.124 - 0.165: 16 0.165 - 0.207: 4 Chirality restraints: 1228 Sorted by residual: chirality pdb=" CA PRO C 168 " pdb=" N PRO C 168 " pdb=" C PRO C 168 " pdb=" CB PRO C 168 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PRO D 168 " pdb=" N PRO D 168 " pdb=" C PRO D 168 " pdb=" CB PRO D 168 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO A 597 " pdb=" N PRO A 597 " pdb=" C PRO A 597 " pdb=" CB PRO A 597 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1225 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 596 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO A 597 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 597 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 597 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 596 " 0.078 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO B 597 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO B 597 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 597 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 167 " 0.062 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO D 168 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO D 168 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 168 " 0.049 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 181 2.68 - 3.23: 8095 3.23 - 3.79: 12964 3.79 - 4.34: 16329 4.34 - 4.90: 26873 Nonbonded interactions: 64442 Sorted by model distance: nonbonded pdb=" OD1 ASP C 130 " pdb=" OH TYR C 155 " model vdw 2.123 3.040 nonbonded pdb=" NH1 ARG A 467 " pdb=" O LEU A 489 " model vdw 2.159 3.120 nonbonded pdb=" ND2 ASN B 473 " pdb=" OD1 ASP B 486 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN A 473 " pdb=" OD1 ASP A 486 " model vdw 2.222 3.120 nonbonded pdb=" N GLU D 8 " pdb=" OE1 GLU D 8 " model vdw 2.276 3.120 ... (remaining 64437 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.000 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: 0.050 Set scattering table: 0.090 Process input model: 21.410 Find NCS groups from input model: 0.220 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 0.005 0.110 8176 Z= 0.339 Angle : 0.833 12.908 11026 Z= 0.479 Chirality : 0.043 0.207 1228 Planarity : 0.007 0.117 1402 Dihedral : 17.067 89.696 3104 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.68 % Allowed : 25.62 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.27), residues: 968 helix: 1.33 (0.21), residues: 602 sheet: -0.79 (0.86), residues: 40 loop : -1.15 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 368 HIS 0.006 0.001 HIS B 460 PHE 0.014 0.002 PHE B 527 TYR 0.052 0.003 TYR B 532 ARG 0.010 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7040 (mm-30) REVERT: C 58 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7660 (mmm160) REVERT: C 166 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6672 (tmm) REVERT: B 414 LYS cc_start: 0.7581 (mmmm) cc_final: 0.7224 (mtmm) REVERT: B 425 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 512 MET cc_start: 0.6356 (ttp) cc_final: 0.6123 (ptt) REVERT: B 519 MET cc_start: 0.3185 (mmp) cc_final: 0.2705 (mmp) REVERT: D 186 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7962 (mm-30) outliers start: 6 outliers final: 1 residues processed: 221 average time/residue: 0.2129 time to fit residues: 62.2037 Evaluate side-chains 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain C residue 166 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.0030 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN B 386 GLN B 441 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8176 Z= 0.195 Angle : 0.623 5.975 11026 Z= 0.327 Chirality : 0.040 0.150 1228 Planarity : 0.005 0.064 1402 Dihedral : 4.771 55.632 1089 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.29 % Allowed : 21.20 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.27), residues: 968 helix: 1.80 (0.21), residues: 600 sheet: -0.37 (1.09), residues: 22 loop : -1.22 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 368 HIS 0.002 0.001 HIS A 477 PHE 0.015 0.002 PHE B 525 TYR 0.032 0.002 TYR D 131 ARG 0.008 0.001 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6482 (mt0) cc_final: 0.6153 (mm-40) REVERT: A 512 MET cc_start: 0.6677 (ptt) cc_final: 0.5858 (ptm) REVERT: B 414 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7312 (mtmm) REVERT: B 574 TYR cc_start: 0.5661 (m-10) cc_final: 0.5208 (m-10) REVERT: D 58 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7786 (mmm160) REVERT: D 197 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7802 (tt) REVERT: D 200 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7633 (mp10) outliers start: 29 outliers final: 10 residues processed: 200 average time/residue: 0.2006 time to fit residues: 54.9368 Evaluate side-chains 157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN B 436 GLN B 441 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8176 Z= 0.213 Angle : 0.620 8.194 11026 Z= 0.323 Chirality : 0.040 0.160 1228 Planarity : 0.004 0.045 1402 Dihedral : 4.244 29.942 1086 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.85 % Allowed : 23.02 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.27), residues: 968 helix: 1.71 (0.21), residues: 602 sheet: -0.19 (1.15), residues: 22 loop : -1.27 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 342 HIS 0.002 0.001 HIS A 477 PHE 0.013 0.002 PHE A 599 TYR 0.032 0.002 TYR D 131 ARG 0.008 0.001 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6434 (mt0) cc_final: 0.6113 (mm-40) REVERT: A 409 MET cc_start: 0.8276 (mtp) cc_final: 0.7901 (mtt) REVERT: A 512 MET cc_start: 0.7037 (ptt) cc_final: 0.6206 (ptm) REVERT: C 197 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7774 (tt) REVERT: C 200 GLN cc_start: 0.8236 (pt0) cc_final: 0.7662 (pm20) REVERT: B 409 MET cc_start: 0.8302 (mtp) cc_final: 0.7905 (mtt) REVERT: B 512 MET cc_start: 0.6917 (ptt) cc_final: 0.5990 (ptm) REVERT: D 58 ARG cc_start: 0.8123 (mmt-90) cc_final: 0.7762 (mmm160) REVERT: D 197 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7796 (tt) REVERT: D 200 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7621 (mp10) outliers start: 34 outliers final: 16 residues processed: 193 average time/residue: 0.2014 time to fit residues: 52.3902 Evaluate side-chains 169 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8176 Z= 0.229 Angle : 0.638 7.257 11026 Z= 0.327 Chirality : 0.041 0.174 1228 Planarity : 0.004 0.046 1402 Dihedral : 4.240 31.419 1086 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.65 % Allowed : 21.88 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.27), residues: 968 helix: 1.66 (0.21), residues: 602 sheet: 0.07 (0.98), residues: 34 loop : -1.21 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 342 HIS 0.002 0.001 HIS A 477 PHE 0.019 0.002 PHE B 525 TYR 0.032 0.002 TYR D 131 ARG 0.006 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6475 (mt0) cc_final: 0.6243 (mm-40) REVERT: A 409 MET cc_start: 0.8280 (mtp) cc_final: 0.7925 (mtt) REVERT: A 512 MET cc_start: 0.7104 (ptt) cc_final: 0.6295 (ptm) REVERT: C 197 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7926 (tt) REVERT: C 200 GLN cc_start: 0.8246 (pt0) cc_final: 0.7764 (pt0) REVERT: B 409 MET cc_start: 0.8317 (mtp) cc_final: 0.7932 (mtt) REVERT: B 512 MET cc_start: 0.6964 (ptt) cc_final: 0.6143 (ptm) REVERT: D 58 ARG cc_start: 0.8152 (mmt-90) cc_final: 0.7899 (mmp80) REVERT: D 170 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6605 (t-90) REVERT: D 197 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7804 (tt) REVERT: D 200 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: D 223 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7485 (mp) REVERT: D 224 MET cc_start: 0.7445 (mmm) cc_final: 0.7206 (mmm) outliers start: 41 outliers final: 22 residues processed: 192 average time/residue: 0.2031 time to fit residues: 53.2929 Evaluate side-chains 177 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8176 Z= 0.238 Angle : 0.640 8.711 11026 Z= 0.330 Chirality : 0.041 0.188 1228 Planarity : 0.004 0.047 1402 Dihedral : 4.297 35.276 1086 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.42 % Allowed : 23.36 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.27), residues: 968 helix: 1.65 (0.21), residues: 602 sheet: 1.02 (1.43), residues: 22 loop : -1.30 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 342 HIS 0.002 0.001 HIS A 369 PHE 0.021 0.002 PHE B 525 TYR 0.034 0.002 TYR D 131 ARG 0.010 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6478 (mt0) cc_final: 0.6186 (mm-40) REVERT: A 409 MET cc_start: 0.8278 (mtp) cc_final: 0.7749 (mtt) REVERT: A 512 MET cc_start: 0.7122 (ptt) cc_final: 0.6291 (ptm) REVERT: C 197 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7937 (tt) REVERT: C 200 GLN cc_start: 0.8240 (pt0) cc_final: 0.7776 (pt0) REVERT: B 409 MET cc_start: 0.8274 (mtp) cc_final: 0.7729 (mtt) REVERT: B 512 MET cc_start: 0.6992 (ptt) cc_final: 0.6193 (ptm) REVERT: D 58 ARG cc_start: 0.8181 (mmt-90) cc_final: 0.7943 (mmt-90) REVERT: D 197 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7765 (tt) REVERT: D 200 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: D 223 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7474 (mp) outliers start: 39 outliers final: 24 residues processed: 196 average time/residue: 0.1981 time to fit residues: 53.0345 Evaluate side-chains 178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.0470 chunk 89 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8176 Z= 0.173 Angle : 0.624 10.054 11026 Z= 0.318 Chirality : 0.040 0.158 1228 Planarity : 0.004 0.047 1402 Dihedral : 4.271 39.004 1086 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.06 % Allowed : 24.83 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.27), residues: 968 helix: 1.82 (0.21), residues: 602 sheet: 1.31 (1.44), residues: 22 loop : -1.20 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 342 HIS 0.003 0.001 HIS B 460 PHE 0.015 0.001 PHE B 525 TYR 0.031 0.001 TYR D 131 ARG 0.010 0.000 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8115 (tttp) REVERT: A 386 GLN cc_start: 0.6474 (mt0) cc_final: 0.6201 (mm-40) REVERT: A 409 MET cc_start: 0.8227 (mtp) cc_final: 0.7726 (mtt) REVERT: C 200 GLN cc_start: 0.8265 (pt0) cc_final: 0.7660 (pm20) REVERT: B 367 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8097 (tttp) REVERT: B 409 MET cc_start: 0.8241 (mtp) cc_final: 0.7756 (mtt) REVERT: B 525 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: B 581 MET cc_start: 0.7481 (mmm) cc_final: 0.7189 (mmm) REVERT: D 58 ARG cc_start: 0.8097 (mmt-90) cc_final: 0.7725 (mmm160) REVERT: D 108 ASP cc_start: 0.7193 (t0) cc_final: 0.6970 (t0) REVERT: D 197 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7739 (tt) REVERT: D 200 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7677 (mp10) outliers start: 27 outliers final: 11 residues processed: 180 average time/residue: 0.2059 time to fit residues: 50.2408 Evaluate side-chains 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8176 Z= 0.213 Angle : 0.654 10.516 11026 Z= 0.331 Chirality : 0.042 0.231 1228 Planarity : 0.004 0.047 1402 Dihedral : 4.295 43.385 1086 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.74 % Allowed : 25.17 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.12 (0.27), residues: 968 helix: 1.77 (0.21), residues: 600 sheet: 0.13 (1.03), residues: 34 loop : -1.12 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 342 HIS 0.002 0.000 HIS A 369 PHE 0.012 0.001 PHE B 599 TYR 0.030 0.002 TYR D 131 ARG 0.011 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8132 (tttp) REVERT: A 386 GLN cc_start: 0.6514 (mt0) cc_final: 0.6220 (mm-40) REVERT: A 409 MET cc_start: 0.8245 (mtp) cc_final: 0.7729 (mtt) REVERT: C 170 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6368 (t-90) REVERT: C 197 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7720 (tt) REVERT: C 200 GLN cc_start: 0.8270 (pt0) cc_final: 0.7666 (pm20) REVERT: B 367 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8119 (tttp) REVERT: B 409 MET cc_start: 0.8267 (mtp) cc_final: 0.7774 (mtt) REVERT: B 525 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7040 (m-10) REVERT: B 581 MET cc_start: 0.7515 (mmm) cc_final: 0.7307 (mmm) REVERT: D 58 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7764 (mmm160) REVERT: D 108 ASP cc_start: 0.7204 (t0) cc_final: 0.6989 (t0) REVERT: D 197 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7737 (tt) REVERT: D 200 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: D 223 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7439 (mp) REVERT: D 224 MET cc_start: 0.7598 (mmm) cc_final: 0.7285 (mmm) outliers start: 33 outliers final: 15 residues processed: 177 average time/residue: 0.2017 time to fit residues: 49.0443 Evaluate side-chains 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 367 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 72 optimal weight: 0.0980 chunk 84 optimal weight: 0.0470 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8176 Z= 0.172 Angle : 0.649 11.442 11026 Z= 0.325 Chirality : 0.041 0.241 1228 Planarity : 0.004 0.048 1402 Dihedral : 4.280 48.375 1086 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.95 % Allowed : 26.42 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.27), residues: 968 helix: 1.85 (0.21), residues: 600 sheet: 0.04 (0.99), residues: 34 loop : -1.08 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 342 HIS 0.003 0.000 HIS B 460 PHE 0.008 0.001 PHE B 527 TYR 0.025 0.001 TYR D 131 ARG 0.012 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6494 (mt0) cc_final: 0.6190 (mm-40) REVERT: A 409 MET cc_start: 0.8222 (mtp) cc_final: 0.7744 (mtt) REVERT: C 170 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.6238 (t-90) REVERT: C 197 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7877 (tt) REVERT: C 200 GLN cc_start: 0.8296 (pt0) cc_final: 0.7818 (pt0) REVERT: B 409 MET cc_start: 0.8240 (mtp) cc_final: 0.7740 (mtt) REVERT: B 525 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6892 (m-10) REVERT: B 581 MET cc_start: 0.7452 (mmm) cc_final: 0.7220 (mmm) REVERT: D 12 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7596 (ttm110) REVERT: D 173 ARG cc_start: 0.7501 (ttm170) cc_final: 0.7020 (ttp-170) REVERT: D 197 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7702 (tt) REVERT: D 200 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: D 224 MET cc_start: 0.7681 (mmm) cc_final: 0.7444 (mmm) outliers start: 26 outliers final: 11 residues processed: 186 average time/residue: 0.2057 time to fit residues: 52.0274 Evaluate side-chains 166 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 550 HIS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8176 Z= 0.352 Angle : 0.780 12.779 11026 Z= 0.394 Chirality : 0.047 0.293 1228 Planarity : 0.005 0.059 1402 Dihedral : 4.670 56.298 1086 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.06 % Allowed : 27.21 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.27), residues: 968 helix: 1.52 (0.21), residues: 594 sheet: 0.08 (1.03), residues: 34 loop : -1.03 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 342 HIS 0.006 0.001 HIS A 432 PHE 0.036 0.002 PHE B 599 TYR 0.039 0.003 TYR A 534 ARG 0.013 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6589 (mt0) cc_final: 0.6259 (mm-40) REVERT: A 409 MET cc_start: 0.8296 (mtp) cc_final: 0.7748 (mtt) REVERT: C 170 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6420 (t-90) REVERT: C 197 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7777 (tt) REVERT: C 200 GLN cc_start: 0.8303 (pt0) cc_final: 0.7736 (pm20) REVERT: B 409 MET cc_start: 0.8312 (mtp) cc_final: 0.7784 (mtt) REVERT: B 525 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6924 (m-10) REVERT: D 197 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7757 (tt) REVERT: D 200 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: D 223 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7514 (mp) outliers start: 27 outliers final: 17 residues processed: 183 average time/residue: 0.1927 time to fit residues: 48.4461 Evaluate side-chains 165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 550 HIS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain B residue 626 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8176 Z= 0.224 Angle : 0.757 16.632 11026 Z= 0.371 Chirality : 0.044 0.275 1228 Planarity : 0.004 0.055 1402 Dihedral : 4.635 56.554 1086 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.38 % Allowed : 27.78 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.28), residues: 968 helix: 1.60 (0.21), residues: 594 sheet: 0.15 (1.05), residues: 34 loop : -0.96 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 342 HIS 0.010 0.001 HIS A 460 PHE 0.012 0.001 PHE B 599 TYR 0.036 0.002 TYR A 534 ARG 0.013 0.001 ARG C 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 GLN cc_start: 0.6558 (mt0) cc_final: 0.6252 (mm-40) REVERT: A 409 MET cc_start: 0.8233 (mtp) cc_final: 0.7756 (mtt) REVERT: C 170 HIS cc_start: 0.6720 (OUTLIER) cc_final: 0.6326 (t-90) REVERT: C 197 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7719 (tt) REVERT: C 200 GLN cc_start: 0.8291 (pt0) cc_final: 0.7720 (pm20) REVERT: B 409 MET cc_start: 0.8262 (mtp) cc_final: 0.7760 (mtt) REVERT: B 525 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6851 (m-10) REVERT: D 197 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7737 (tt) REVERT: D 200 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: D 223 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7279 (mp) outliers start: 21 outliers final: 11 residues processed: 171 average time/residue: 0.2186 time to fit residues: 51.9100 Evaluate side-chains 163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 170 HIS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 550 HIS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 601 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.0040 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.197137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163165 restraints weight = 11334.777| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.67 r_work: 0.3879 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8176 Z= 0.200 Angle : 0.759 18.933 11026 Z= 0.367 Chirality : 0.043 0.272 1228 Planarity : 0.004 0.056 1402 Dihedral : 4.212 17.925 1084 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.93 % Allowed : 28.68 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.28), residues: 968 helix: 1.70 (0.21), residues: 594 sheet: 0.09 (1.02), residues: 34 loop : -0.98 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 342 HIS 0.009 0.001 HIS A 460 PHE 0.010 0.001 PHE B 599 TYR 0.034 0.002 TYR B 534 ARG 0.013 0.001 ARG C 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.93 seconds wall clock time: 36 minutes 26.14 seconds (2186.14 seconds total)