Starting phenix.real_space_refine on Tue Feb 13 15:13:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hio_34824/02_2024/8hio_34824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hio_34824/02_2024/8hio_34824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hio_34824/02_2024/8hio_34824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hio_34824/02_2024/8hio_34824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hio_34824/02_2024/8hio_34824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hio_34824/02_2024/8hio_34824.pdb" } resolution = 3.73 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 ------------------------------------------------------------------------------- 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= 0.012 sd= 0.211 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 47 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 3952 2.51 5 N 1281 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6681 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1019 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 12} Link IDs: {'rna2p': 15, 'rna3p': 31} Chain: "A" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4436 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 543} Chain breaks: 2 Chain: "D" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1224 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5151 SG CYS A 552 106.496 33.507 50.395 1.00185.32 S ATOM 5284 SG CYS A 569 106.415 36.312 50.252 1.00190.90 S ATOM 5302 SG CYS A 572 107.743 36.523 47.525 1.00196.84 S Time building chain proxies: 4.25, per 1000 atoms: 0.64 Number of scatterers: 6681 At special positions: 0 Unit cell: (118.101, 99.603, 102.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 47 15.00 Mg 1 11.99 O 1378 8.00 N 1281 7.00 C 3952 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 - 3.50 Amino acid : False - 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: 3.03 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 569 " Number of angles added : 3 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 61.3% alpha, 12.2% beta 11 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 18 through 52 Processing helix chain 'A' and resid 53 through 85 Processing helix chain 'A' and resid 92 through 119 Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.501A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.575A pdb=" N ARG A 345 " --> pdb=" O PHE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 397 Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.602A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 479 removed outlier: 3.710A pdb=" N TRP A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 518 through 534 removed outlier: 4.114A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.744A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'D' and resid 19 through 52 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 96 through 118 removed outlier: 3.640A pdb=" N ALA D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 145 removed outlier: 3.519A pdb=" N TYR D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 176 removed outlier: 3.598A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 195 removed outlier: 6.716A pdb=" N THR A 299 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 281 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS A 297 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 283 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 295 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 285 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 293 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A 287 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 11 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE A 262 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG A 251 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 264 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 266 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR A 247 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 removed outlier: 5.947A pdb=" N ALA A 328 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 361 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323 removed outlier: 4.142A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568 374 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1691 1.33 - 1.45: 1571 1.45 - 1.57: 3522 1.57 - 1.69: 93 1.69 - 1.81: 33 Bond restraints: 6910 Sorted by residual: bond pdb=" C TRP A 261 " pdb=" N ILE A 262 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.34e-02 5.57e+03 4.96e+00 bond pdb=" C ASP A 477 " pdb=" N GLN A 478 " ideal model delta sigma weight residual 1.332 1.311 0.022 1.40e-02 5.10e+03 2.40e+00 bond pdb=" CG LEU A 221 " pdb=" CD1 LEU A 221 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB VAL A 194 " pdb=" CG1 VAL A 194 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB PHE A 443 " pdb=" CG PHE A 443 " ideal model delta sigma weight residual 1.502 1.477 0.025 2.30e-02 1.89e+03 1.22e+00 ... (remaining 6905 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.57: 330 105.57 - 112.70: 3901 112.70 - 119.82: 2252 119.82 - 126.94: 2891 126.94 - 134.07: 227 Bond angle restraints: 9601 Sorted by residual: angle pdb=" N TRP A 440 " pdb=" CA TRP A 440 " pdb=" C TRP A 440 " ideal model delta sigma weight residual 113.12 108.77 4.35 1.25e+00 6.40e-01 1.21e+01 angle pdb=" CA LEU A 369 " pdb=" CB LEU A 369 " pdb=" CG LEU A 369 " ideal model delta sigma weight residual 116.30 107.20 9.10 3.50e+00 8.16e-02 6.75e+00 angle pdb=" C LEU A 318 " pdb=" N GLY A 319 " pdb=" CA GLY A 319 " ideal model delta sigma weight residual 120.51 124.36 -3.85 1.63e+00 3.76e-01 5.57e+00 angle pdb=" C GLN A 453 " pdb=" N GLU A 454 " pdb=" CA GLU A 454 " ideal model delta sigma weight residual 122.42 118.79 3.63 1.55e+00 4.16e-01 5.48e+00 angle pdb=" C ALA A 281 " pdb=" N GLU A 282 " pdb=" CA GLU A 282 " ideal model delta sigma weight residual 122.99 119.73 3.26 1.41e+00 5.03e-01 5.34e+00 ... (remaining 9596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.19: 3719 19.19 - 38.38: 318 38.38 - 57.58: 133 57.58 - 76.77: 68 76.77 - 95.96: 4 Dihedral angle restraints: 4242 sinusoidal: 2150 harmonic: 2092 Sorted by residual: dihedral pdb=" O4' U B 6 " pdb=" C1' U B 6 " pdb=" N1 U B 6 " pdb=" C2 U B 6 " ideal model delta sinusoidal sigma weight residual -160.00 -83.79 -76.21 1 1.50e+01 4.44e-03 3.25e+01 dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -171.33 65.33 1 1.70e+01 3.46e-03 1.94e+01 dihedral pdb=" O4' C B 15 " pdb=" C1' C B 15 " pdb=" N1 C B 15 " pdb=" C2 C B 15 " ideal model delta sinusoidal sigma weight residual -160.00 -104.45 -55.55 1 1.50e+01 4.44e-03 1.85e+01 ... (remaining 4239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 688 0.029 - 0.058: 282 0.058 - 0.087: 86 0.087 - 0.115: 30 0.115 - 0.144: 10 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL A 268 " pdb=" N VAL A 268 " pdb=" C VAL A 268 " pdb=" CB VAL A 268 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL A 361 " pdb=" N VAL A 361 " pdb=" C VAL A 361 " pdb=" CB VAL A 361 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1093 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C GLN A 452 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN A 452 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 453 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 472 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ALA A 472 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 472 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 473 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 459 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LYS A 459 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 459 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA A 460 " 0.011 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 30 2.38 - 3.01: 3883 3.01 - 3.64: 10567 3.64 - 4.27: 15151 4.27 - 4.90: 24433 Nonbonded interactions: 54064 Sorted by model distance: nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 1.744 2.170 nonbonded pdb=" OP2 C B -21 " pdb="MG MG B 101 " model vdw 1.992 2.170 nonbonded pdb=" OP1 G B -7 " pdb=" NZ LYS A 14 " model vdw 2.111 2.520 nonbonded pdb=" OD2 ASP A 466 " pdb=" NE2 GLN A 470 " model vdw 2.147 2.520 nonbonded pdb=" O TRP A 428 " pdb=" OG SER A 436 " model vdw 2.153 2.440 ... (remaining 54059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.050 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.370 Find NCS groups from input model: 0.160 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 0.042 6910 Z= 0.352 Angle : 0.664 9.097 9601 Z= 0.363 Chirality : 0.037 0.144 1096 Planarity : 0.004 0.031 1072 Dihedral : 18.515 95.962 2880 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.22 (0.32), residues: 707 helix: 2.70 (0.25), residues: 421 sheet: -0.24 (0.58), residues: 75 loop : -0.43 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 320 HIS 0.009 0.002 HIS A 7 PHE 0.008 0.001 PHE A 443 TYR 0.019 0.002 TYR A 217 ARG 0.005 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 138 LYS cc_start: 0.8899 (tttt) cc_final: 0.8609 (tmtt) REVERT: A 169 ILE cc_start: 0.8917 (mm) cc_final: 0.8404 (tp) REVERT: A 333 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7792 (tpp80) REVERT: A 356 SER cc_start: 0.7773 (t) cc_final: 0.7543 (p) REVERT: A 420 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.5416 (mpp-170) REVERT: A 530 MET cc_start: 0.8057 (mmt) cc_final: 0.7515 (mmm) REVERT: D 27 LEU cc_start: 0.9226 (mt) cc_final: 0.8976 (mt) REVERT: D 32 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8005 (ttp-170) REVERT: D 42 TYR cc_start: 0.8057 (t80) cc_final: 0.7857 (t80) REVERT: D 46 LEU cc_start: 0.9019 (mt) cc_final: 0.8653 (mt) REVERT: D 50 TRP cc_start: 0.8448 (m100) cc_final: 0.8030 (m100) REVERT: D 98 ARG cc_start: 0.4191 (mtt180) cc_final: 0.3519 (tpm170) REVERT: D 115 ILE cc_start: 0.4875 (mt) cc_final: 0.4406 (mt) REVERT: D 127 LYS cc_start: 0.9577 (tppt) cc_final: 0.9344 (tptp) REVERT: D 163 LYS cc_start: 0.8615 (mttt) cc_final: 0.8395 (mmtt) REVERT: D 185 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7354 (mtp180) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3001 time to fit residues: 67.1876 Evaluate side-chains 121 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.0040 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 449 GLN A 516 HIS D 39 GLN D 143 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6910 Z= 0.253 Angle : 0.613 6.899 9601 Z= 0.323 Chirality : 0.038 0.173 1096 Planarity : 0.004 0.044 1072 Dihedral : 18.753 95.575 1546 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.44 % Allowed : 19.45 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.45 (0.33), residues: 707 helix: 2.78 (0.24), residues: 427 sheet: -0.07 (0.61), residues: 73 loop : -0.24 (0.47), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 450 HIS 0.012 0.002 HIS D 161 PHE 0.007 0.001 PHE A 582 TYR 0.016 0.002 TYR A 217 ARG 0.011 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8249 (mtt) cc_final: 0.7938 (mtm) REVERT: A 32 ARG cc_start: 0.6394 (ttp80) cc_final: 0.5934 (ttp80) REVERT: A 119 LYS cc_start: 0.9213 (ttpp) cc_final: 0.9008 (tptp) REVERT: A 138 LYS cc_start: 0.8872 (tttt) cc_final: 0.8547 (tmtt) REVERT: A 169 ILE cc_start: 0.8696 (mm) cc_final: 0.8086 (tp) REVERT: A 356 SER cc_start: 0.7764 (t) cc_final: 0.7502 (p) REVERT: A 420 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.5197 (mpp-170) REVERT: D 23 GLN cc_start: 0.8844 (tp40) cc_final: 0.8598 (mt0) REVERT: D 32 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8019 (ttp-170) REVERT: D 42 TYR cc_start: 0.8098 (t80) cc_final: 0.7818 (t80) REVERT: D 46 LEU cc_start: 0.9136 (mt) cc_final: 0.8694 (mm) REVERT: D 138 LYS cc_start: 0.9435 (mttt) cc_final: 0.9116 (mttp) REVERT: D 167 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8109 (mmmt) REVERT: D 185 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7386 (mtm180) outliers start: 20 outliers final: 11 residues processed: 138 average time/residue: 0.2610 time to fit residues: 44.2035 Evaluate side-chains 120 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.0020 chunk 21 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 0.0030 chunk 18 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 516 HIS ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 143 GLN D 184 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6910 Z= 0.248 Angle : 0.604 7.124 9601 Z= 0.313 Chirality : 0.038 0.246 1096 Planarity : 0.004 0.036 1072 Dihedral : 18.649 93.342 1546 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.61 % Allowed : 21.34 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.33), residues: 707 helix: 2.81 (0.24), residues: 426 sheet: -0.08 (0.61), residues: 77 loop : 0.02 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 450 HIS 0.010 0.002 HIS A 554 PHE 0.007 0.001 PHE A 582 TYR 0.015 0.002 TYR A 217 ARG 0.007 0.001 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8280 (mtt) cc_final: 0.7955 (mtm) REVERT: A 29 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7349 (t-90) REVERT: A 63 MET cc_start: 0.9012 (ptp) cc_final: 0.8599 (ptt) REVERT: A 138 LYS cc_start: 0.8843 (tttt) cc_final: 0.8526 (tmtt) REVERT: A 260 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8364 (mm110) REVERT: A 333 ARG cc_start: 0.8244 (ttt180) cc_final: 0.7756 (tpp80) REVERT: A 356 SER cc_start: 0.7807 (t) cc_final: 0.7518 (p) REVERT: A 578 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: D 23 GLN cc_start: 0.8922 (tp40) cc_final: 0.8589 (mt0) REVERT: D 32 ARG cc_start: 0.8513 (ttp80) cc_final: 0.8195 (ttm170) REVERT: D 42 TYR cc_start: 0.8019 (t80) cc_final: 0.7805 (t80) REVERT: D 127 LYS cc_start: 0.9455 (tppt) cc_final: 0.9119 (tppt) REVERT: D 132 GLN cc_start: 0.9038 (mt0) cc_final: 0.8831 (mp10) REVERT: D 167 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8168 (mmmt) REVERT: D 185 ARG cc_start: 0.8312 (mmm160) cc_final: 0.7376 (mtp180) outliers start: 21 outliers final: 11 residues processed: 130 average time/residue: 0.2242 time to fit residues: 37.3150 Evaluate side-chains 111 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 578 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 40.0000 chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 40.0000 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 143 GLN D 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6910 Z= 0.222 Angle : 0.593 7.856 9601 Z= 0.305 Chirality : 0.036 0.161 1096 Planarity : 0.004 0.034 1072 Dihedral : 18.618 92.641 1546 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.13 % Allowed : 21.34 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.33), residues: 707 helix: 2.75 (0.24), residues: 426 sheet: 0.07 (0.71), residues: 63 loop : -0.06 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 50 HIS 0.012 0.002 HIS D 29 PHE 0.010 0.001 PHE A 582 TYR 0.014 0.002 TYR D 141 ARG 0.005 0.001 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8199 (mtt) cc_final: 0.7883 (mtm) REVERT: A 26 TRP cc_start: 0.8320 (t60) cc_final: 0.7024 (t60) REVERT: A 29 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7266 (t-90) REVERT: A 63 MET cc_start: 0.8997 (ptp) cc_final: 0.8547 (ptt) REVERT: A 138 LYS cc_start: 0.8952 (tttt) cc_final: 0.8606 (tmtt) REVERT: A 194 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7536 (p) REVERT: A 356 SER cc_start: 0.7782 (t) cc_final: 0.7450 (p) REVERT: A 530 MET cc_start: 0.7866 (mmp) cc_final: 0.7665 (mmm) REVERT: D 42 TYR cc_start: 0.7928 (t80) cc_final: 0.7698 (t80) REVERT: D 127 LYS cc_start: 0.9444 (tppt) cc_final: 0.9095 (tppt) REVERT: D 167 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8221 (mmmt) REVERT: D 184 HIS cc_start: 0.6331 (m90) cc_final: 0.6130 (m90) REVERT: D 185 ARG cc_start: 0.8339 (mmm160) cc_final: 0.7360 (mtm180) outliers start: 24 outliers final: 14 residues processed: 126 average time/residue: 0.2346 time to fit residues: 37.3965 Evaluate side-chains 109 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6910 Z= 0.203 Angle : 0.582 7.268 9601 Z= 0.304 Chirality : 0.037 0.256 1096 Planarity : 0.004 0.039 1072 Dihedral : 18.558 92.813 1546 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.79 % Allowed : 23.06 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.39 (0.33), residues: 707 helix: 2.66 (0.24), residues: 426 sheet: 0.07 (0.71), residues: 63 loop : -0.14 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 50 HIS 0.011 0.001 HIS D 29 PHE 0.005 0.001 PHE A 582 TYR 0.012 0.001 TYR A 217 ARG 0.006 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8033 (mtt) cc_final: 0.7715 (mtm) REVERT: A 29 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7230 (t-90) REVERT: A 63 MET cc_start: 0.9053 (ptp) cc_final: 0.8366 (ptp) REVERT: A 138 LYS cc_start: 0.8942 (tttt) cc_final: 0.8589 (tmtt) REVERT: A 194 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7666 (p) REVERT: A 356 SER cc_start: 0.7760 (t) cc_final: 0.7437 (p) REVERT: D 42 TYR cc_start: 0.7889 (t80) cc_final: 0.7594 (t80) REVERT: D 132 GLN cc_start: 0.8971 (mt0) cc_final: 0.8740 (mp10) REVERT: D 185 ARG cc_start: 0.8374 (mmm160) cc_final: 0.7290 (mtm180) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 0.2088 time to fit residues: 31.2803 Evaluate side-chains 111 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 449 GLN A 452 GLN ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 137 GLN D 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6910 Z= 0.340 Angle : 0.666 9.964 9601 Z= 0.341 Chirality : 0.038 0.161 1096 Planarity : 0.005 0.036 1072 Dihedral : 18.633 92.618 1546 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.30 % Allowed : 23.58 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.10 (0.32), residues: 707 helix: 2.41 (0.24), residues: 426 sheet: 0.05 (0.74), residues: 61 loop : -0.22 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 50 HIS 0.009 0.002 HIS D 29 PHE 0.007 0.001 PHE A 155 TYR 0.018 0.002 TYR A 217 ARG 0.006 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8416 (mtt) cc_final: 0.8046 (mtm) REVERT: A 11 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8297 (t) REVERT: A 29 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7447 (t-90) REVERT: A 44 ASP cc_start: 0.8842 (p0) cc_final: 0.8626 (p0) REVERT: A 63 MET cc_start: 0.9057 (ptp) cc_final: 0.8300 (ptp) REVERT: A 104 LEU cc_start: 0.9673 (tt) cc_final: 0.9270 (mt) REVERT: A 138 LYS cc_start: 0.8966 (tttt) cc_final: 0.8603 (tmtt) REVERT: A 185 ARG cc_start: 0.6251 (mtm180) cc_final: 0.6030 (mtt180) REVERT: A 356 SER cc_start: 0.7829 (t) cc_final: 0.7480 (p) REVERT: D 42 TYR cc_start: 0.7877 (t80) cc_final: 0.7295 (t80) REVERT: D 181 LEU cc_start: 0.7723 (tp) cc_final: 0.7236 (pt) REVERT: D 185 ARG cc_start: 0.8499 (mmm160) cc_final: 0.7330 (mtm180) REVERT: D 258 GLN cc_start: 0.6843 (tm-30) cc_final: 0.6505 (tm-30) outliers start: 25 outliers final: 19 residues processed: 115 average time/residue: 0.2119 time to fit residues: 31.6992 Evaluate side-chains 112 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6910 Z= 0.244 Angle : 0.634 16.515 9601 Z= 0.320 Chirality : 0.037 0.162 1096 Planarity : 0.004 0.035 1072 Dihedral : 18.548 92.928 1546 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.82 % Allowed : 23.75 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.03 (0.33), residues: 707 helix: 2.36 (0.25), residues: 426 sheet: -0.02 (0.73), residues: 61 loop : -0.25 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 50 HIS 0.010 0.002 HIS D 29 PHE 0.005 0.001 PHE A 155 TYR 0.030 0.002 TYR A 576 ARG 0.005 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8345 (mtt) cc_final: 0.7978 (mtm) REVERT: A 11 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8237 (t) REVERT: A 26 TRP cc_start: 0.8127 (t60) cc_final: 0.6686 (t60) REVERT: A 29 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7203 (t-90) REVERT: A 44 ASP cc_start: 0.8862 (p0) cc_final: 0.8605 (p0) REVERT: A 63 MET cc_start: 0.9015 (ptp) cc_final: 0.8180 (ptp) REVERT: A 356 SER cc_start: 0.7747 (t) cc_final: 0.7402 (p) REVERT: D 42 TYR cc_start: 0.7849 (t80) cc_final: 0.7174 (t80) REVERT: D 185 ARG cc_start: 0.8521 (mmm160) cc_final: 0.7360 (mtm180) outliers start: 28 outliers final: 21 residues processed: 112 average time/residue: 0.2089 time to fit residues: 30.7874 Evaluate side-chains 109 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 138 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 143 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6910 Z= 0.297 Angle : 0.677 16.306 9601 Z= 0.341 Chirality : 0.038 0.161 1096 Planarity : 0.004 0.035 1072 Dihedral : 18.576 92.537 1546 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.82 % Allowed : 24.78 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.85 (0.33), residues: 707 helix: 2.29 (0.25), residues: 426 sheet: -0.33 (0.73), residues: 61 loop : -0.42 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 50 HIS 0.010 0.002 HIS D 29 PHE 0.007 0.001 PHE A 155 TYR 0.032 0.002 TYR A 576 ARG 0.008 0.001 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8319 (mtt) cc_final: 0.7884 (mtm) REVERT: A 11 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 29 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7349 (t-90) REVERT: A 44 ASP cc_start: 0.8924 (p0) cc_final: 0.8645 (p0) REVERT: A 63 MET cc_start: 0.9128 (ptp) cc_final: 0.8266 (ptp) REVERT: A 138 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8819 (tptt) REVERT: A 356 SER cc_start: 0.7772 (t) cc_final: 0.7424 (p) REVERT: D 23 GLN cc_start: 0.9002 (tp40) cc_final: 0.8626 (pt0) REVERT: D 42 TYR cc_start: 0.7916 (t80) cc_final: 0.7240 (t80) REVERT: D 50 TRP cc_start: 0.8180 (m100) cc_final: 0.7966 (m100) REVERT: D 115 ILE cc_start: 0.3484 (mt) cc_final: 0.3266 (mt) REVERT: D 185 ARG cc_start: 0.8656 (mmm160) cc_final: 0.7468 (mtm180) outliers start: 28 outliers final: 22 residues processed: 111 average time/residue: 0.2023 time to fit residues: 29.3363 Evaluate side-chains 110 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 44 optimal weight: 0.5980 chunk 71 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 143 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6910 Z= 0.276 Angle : 0.657 16.871 9601 Z= 0.331 Chirality : 0.038 0.158 1096 Planarity : 0.004 0.038 1072 Dihedral : 18.516 92.690 1546 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.82 % Allowed : 24.78 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.85 (0.33), residues: 707 helix: 2.31 (0.25), residues: 426 sheet: -0.54 (0.72), residues: 61 loop : -0.39 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 450 HIS 0.009 0.002 HIS D 29 PHE 0.006 0.001 PHE A 155 TYR 0.015 0.002 TYR A 217 ARG 0.005 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8336 (mtt) cc_final: 0.7949 (mtm) REVERT: A 11 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8237 (t) REVERT: A 26 TRP cc_start: 0.8136 (t60) cc_final: 0.6679 (t60) REVERT: A 29 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7237 (t-90) REVERT: A 44 ASP cc_start: 0.8929 (p0) cc_final: 0.8646 (p0) REVERT: A 63 MET cc_start: 0.9174 (ptp) cc_final: 0.8835 (ptp) REVERT: A 138 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8882 (tptt) REVERT: A 356 SER cc_start: 0.7717 (t) cc_final: 0.7388 (p) REVERT: D 23 GLN cc_start: 0.9020 (tp40) cc_final: 0.8619 (pt0) REVERT: D 42 TYR cc_start: 0.7985 (t80) cc_final: 0.7398 (t80) REVERT: D 50 TRP cc_start: 0.7932 (m100) cc_final: 0.7574 (m100) REVERT: D 115 ILE cc_start: 0.3161 (mt) cc_final: 0.2921 (mt) REVERT: D 185 ARG cc_start: 0.8686 (mmm160) cc_final: 0.7448 (mtp180) outliers start: 28 outliers final: 23 residues processed: 110 average time/residue: 0.1893 time to fit residues: 27.9157 Evaluate side-chains 114 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 50.0000 chunk 68 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6910 Z= 0.182 Angle : 0.643 16.740 9601 Z= 0.319 Chirality : 0.038 0.279 1096 Planarity : 0.004 0.035 1072 Dihedral : 18.445 92.793 1546 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.75 % Allowed : 27.02 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.93 (0.33), residues: 707 helix: 2.35 (0.25), residues: 432 sheet: -0.39 (0.73), residues: 62 loop : -0.42 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 450 HIS 0.010 0.001 HIS D 29 PHE 0.006 0.001 PHE A 582 TYR 0.012 0.001 TYR D 42 ARG 0.004 0.000 ARG A 568 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8207 (mtt) cc_final: 0.7863 (mtm) REVERT: A 11 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8160 (t) REVERT: A 29 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7092 (t-90) REVERT: A 44 ASP cc_start: 0.8916 (p0) cc_final: 0.8639 (p0) REVERT: A 63 MET cc_start: 0.9106 (ptp) cc_final: 0.8790 (ptp) REVERT: A 138 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8817 (tptt) REVERT: A 194 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7582 (p) REVERT: A 356 SER cc_start: 0.7629 (t) cc_final: 0.7417 (p) REVERT: A 556 ASN cc_start: 0.8596 (m110) cc_final: 0.8331 (m-40) REVERT: D 23 GLN cc_start: 0.9006 (tp40) cc_final: 0.8712 (mp10) REVERT: D 42 TYR cc_start: 0.8152 (t80) cc_final: 0.7288 (t80) REVERT: D 50 TRP cc_start: 0.7767 (m100) cc_final: 0.7453 (m100) REVERT: D 115 ILE cc_start: 0.3587 (mt) cc_final: 0.3313 (mt) REVERT: D 133 LEU cc_start: 0.9339 (tp) cc_final: 0.9129 (tp) REVERT: D 137 GLN cc_start: 0.9067 (mp10) cc_final: 0.8583 (pm20) REVERT: D 159 LEU cc_start: 0.9341 (tp) cc_final: 0.8995 (pp) REVERT: D 185 ARG cc_start: 0.8591 (mmm160) cc_final: 0.7426 (mtm180) outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.2096 time to fit residues: 28.3067 Evaluate side-chains 105 residues out of total 581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 132 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.173388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.133322 restraints weight = 14135.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.137781 restraints weight = 7416.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.140698 restraints weight = 5019.884| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6910 Z= 0.254 Angle : 0.661 16.831 9601 Z= 0.331 Chirality : 0.038 0.235 1096 Planarity : 0.004 0.040 1072 Dihedral : 18.481 91.566 1546 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.27 % Allowed : 26.51 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.84 (0.33), residues: 707 helix: 2.31 (0.25), residues: 432 sheet: -0.52 (0.72), residues: 62 loop : -0.51 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 450 HIS 0.009 0.002 HIS D 29 PHE 0.009 0.001 PHE A 582 TYR 0.018 0.002 TYR D 141 ARG 0.005 0.000 ARG A 568 =============================================================================== Job complete usr+sys time: 1437.96 seconds wall clock time: 26 minutes 53.92 seconds (1613.92 seconds total)