Starting phenix.real_space_refine on Wed Mar 5 21:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsm_18636/03_2025/8qsm_18636.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsm_18636/03_2025/8qsm_18636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsm_18636/03_2025/8qsm_18636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsm_18636/03_2025/8qsm_18636.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsm_18636/03_2025/8qsm_18636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsm_18636/03_2025/8qsm_18636.cif" } resolution = 3.69 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2377 2.51 5 N 573 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3579 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3579 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 18, 'TRANS': 445} Chain breaks: 3 Time building chain proxies: 2.71, per 1000 atoms: 0.76 Number of scatterers: 3579 At special positions: 0 Unit cell: (80.465, 70.015, 65.835, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 609 8.00 N 573 7.00 C 2377 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: 0.89 Conformation dependent library (CDL) restraints added in 411.5 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 83.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 33 through 57 removed outlier: 4.287A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.899A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 156 through 183 removed outlier: 4.226A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.629A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.818A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 246 removed outlier: 3.931A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.638A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.954A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 347 removed outlier: 3.942A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 3.691A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 349 No H-bonds generated for 'chain 'A' and resid 348 through 349' Processing helix chain 'A' and resid 365 through 366 No H-bonds generated for 'chain 'A' and resid 365 through 366' Processing helix chain 'A' and resid 367 through 396 removed outlier: 3.958A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 5.109A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.528A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 4.034A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 484 through 510 Processing helix chain 'A' and resid 531 through 560 removed outlier: 3.573A pdb=" N HIS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439 281 hydrogen bonds defined for protein. 837 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: 0.92 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1081 1.34 - 1.46: 817 1.46 - 1.58: 1743 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3672 Sorted by residual: bond pdb=" CB PRO A 399 " pdb=" CG PRO A 399 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.11e-01 bond pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 1.523 1.531 -0.008 9.20e-03 1.18e+04 7.12e-01 bond pdb=" C VAL A 246 " pdb=" O VAL A 246 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.67e-01 bond pdb=" CB PRO A 306 " pdb=" CG PRO A 306 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.05e-01 bond pdb=" N VAL A 322 " pdb=" CA VAL A 322 " ideal model delta sigma weight residual 1.463 1.470 -0.007 1.18e-02 7.18e+03 4.00e-01 ... (remaining 3667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 4860 1.18 - 2.36: 89 2.36 - 3.55: 23 3.55 - 4.73: 7 4.73 - 5.91: 6 Bond angle restraints: 4985 Sorted by residual: angle pdb=" C PHE A 247 " pdb=" N ILE A 248 " pdb=" CA ILE A 248 " ideal model delta sigma weight residual 121.97 125.78 -3.81 1.80e+00 3.09e-01 4.48e+00 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 113.00 110.27 2.73 1.30e+00 5.92e-01 4.42e+00 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.79e+00 angle pdb=" N ALA A 468 " pdb=" CA ALA A 468 " pdb=" C ALA A 468 " ideal model delta sigma weight residual 111.02 113.92 -2.90 1.52e+00 4.33e-01 3.64e+00 ... (remaining 4980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 1970 14.62 - 29.24: 99 29.24 - 43.87: 29 43.87 - 58.49: 8 58.49 - 73.11: 2 Dihedral angle restraints: 2108 sinusoidal: 785 harmonic: 1323 Sorted by residual: dihedral pdb=" CA THR A 308 " pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " pdb=" CD ARG A 33 " ideal model delta sinusoidal sigma weight residual -60.00 -115.47 55.47 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA ARG A 104 " pdb=" CB ARG A 104 " pdb=" CG ARG A 104 " pdb=" CD ARG A 104 " ideal model delta sinusoidal sigma weight residual 180.00 127.75 52.25 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 2105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 389 0.025 - 0.050: 100 0.050 - 0.075: 55 0.075 - 0.101: 24 0.101 - 0.126: 6 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 571 not shown) Planarity restraints: 611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 238 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL A 238 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL A 238 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 239 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 239 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C VAL A 239 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 239 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 240 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 237 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C PHE A 237 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE A 237 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 238 " -0.009 2.00e-02 2.50e+03 ... (remaining 608 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 887 2.80 - 3.32: 3828 3.32 - 3.85: 5935 3.85 - 4.37: 6627 4.37 - 4.90: 11289 Nonbonded interactions: 28566 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG SER A 267 " model vdw 2.269 3.040 nonbonded pdb=" O ILE A 461 " pdb=" OG SER A 464 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.305 3.040 nonbonded pdb=" O LYS A 262 " pdb=" OG1 THR A 265 " model vdw 2.316 3.040 nonbonded pdb=" O CYS A 242 " pdb=" OG SER A 245 " model vdw 2.326 3.040 ... (remaining 28561 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: 1.050 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.002 0.045 3672 Z= 0.125 Angle : 0.482 5.910 4985 Z= 0.259 Chirality : 0.034 0.126 574 Planarity : 0.004 0.029 611 Dihedral : 10.371 73.110 1262 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.75 % Allowed : 6.17 % Favored : 90.08 % 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: 2.22 (0.41), residues: 456 helix: 2.29 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.69 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 332 HIS 0.001 0.000 HIS A 348 PHE 0.009 0.001 PHE A 198 TYR 0.006 0.001 TYR A 52 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6378 (mtm-85) REVERT: A 47 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 91 PHE cc_start: 0.8867 (m-80) cc_final: 0.8633 (m-10) REVERT: A 198 PHE cc_start: 0.9093 (t80) cc_final: 0.8810 (t80) REVERT: A 200 TRP cc_start: 0.9106 (t60) cc_final: 0.8447 (t60) REVERT: A 313 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8762 (mm-30) REVERT: A 342 TYR cc_start: 0.8881 (m-10) cc_final: 0.8544 (m-80) REVERT: A 369 LEU cc_start: 0.8694 (mt) cc_final: 0.8279 (mt) REVERT: A 427 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8142 (mt) REVERT: A 451 LEU cc_start: 0.9317 (tp) cc_final: 0.9072 (mp) REVERT: A 454 GLN cc_start: 0.8734 (tp40) cc_final: 0.8242 (tp40) REVERT: A 457 GLN cc_start: 0.7944 (pt0) cc_final: 0.6272 (pt0) REVERT: A 474 GLU cc_start: 0.8871 (mt-10) cc_final: 0.7895 (mt-10) REVERT: A 535 TYR cc_start: 0.8767 (t80) cc_final: 0.8253 (t80) outliers start: 14 outliers final: 3 residues processed: 181 average time/residue: 0.1708 time to fit residues: 36.9992 Evaluate side-chains 105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.4980 chunk 34 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 521 HIS ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.097800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083656 restraints weight = 13324.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085902 restraints weight = 7645.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087490 restraints weight = 5122.218| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3672 Z= 0.199 Angle : 0.727 10.213 4985 Z= 0.342 Chirality : 0.040 0.168 574 Planarity : 0.005 0.053 611 Dihedral : 5.718 54.646 502 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.49 % Allowed : 18.50 % Favored : 78.02 % 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: 2.29 (0.40), residues: 456 helix: 2.31 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -1.84 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 69 HIS 0.003 0.001 HIS A 521 PHE 0.034 0.002 PHE A 417 TYR 0.014 0.002 TYR A 444 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6549 (ptp-170) REVERT: A 91 PHE cc_start: 0.8880 (m-80) cc_final: 0.8641 (m-10) REVERT: A 200 TRP cc_start: 0.9099 (t60) cc_final: 0.8435 (t60) REVERT: A 235 LEU cc_start: 0.9525 (mt) cc_final: 0.8956 (tp) REVERT: A 301 MET cc_start: 0.5913 (tpt) cc_final: 0.5674 (tmm) REVERT: A 331 TYR cc_start: 0.9000 (t80) cc_final: 0.8539 (t80) REVERT: A 369 LEU cc_start: 0.8989 (mt) cc_final: 0.8542 (mt) REVERT: A 427 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8448 (mt) REVERT: A 451 LEU cc_start: 0.9305 (tp) cc_final: 0.9068 (mp) REVERT: A 535 TYR cc_start: 0.8869 (t80) cc_final: 0.8456 (t80) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 0.1126 time to fit residues: 17.2015 Evaluate side-chains 101 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 532 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082535 restraints weight = 13460.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084677 restraints weight = 7914.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.086106 restraints weight = 5415.372| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3672 Z= 0.197 Angle : 0.712 11.285 4985 Z= 0.334 Chirality : 0.041 0.171 574 Planarity : 0.005 0.055 611 Dihedral : 5.776 54.742 500 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.90 % Allowed : 19.57 % Favored : 74.53 % 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: 1.99 (0.40), residues: 456 helix: 2.03 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.86 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 69 HIS 0.001 0.000 HIS A 521 PHE 0.043 0.002 PHE A 372 TYR 0.016 0.002 TYR A 335 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6494 (ptp-170) REVERT: A 200 TRP cc_start: 0.9147 (t60) cc_final: 0.8481 (t60) REVERT: A 213 ILE cc_start: 0.9373 (mm) cc_final: 0.9166 (tp) REVERT: A 301 MET cc_start: 0.6216 (tpt) cc_final: 0.5962 (tmm) REVERT: A 307 PHE cc_start: 0.3930 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: A 310 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 331 TYR cc_start: 0.8940 (t80) cc_final: 0.8649 (t80) REVERT: A 369 LEU cc_start: 0.9149 (mt) cc_final: 0.8794 (mt) REVERT: A 454 GLN cc_start: 0.8762 (tp40) cc_final: 0.8276 (tp40) REVERT: A 474 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8193 (mt-10) REVERT: A 535 TYR cc_start: 0.8802 (t80) cc_final: 0.8452 (t80) outliers start: 22 outliers final: 11 residues processed: 117 average time/residue: 0.1045 time to fit residues: 16.1290 Evaluate side-chains 108 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.096787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.083335 restraints weight = 13614.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085464 restraints weight = 7938.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.086963 restraints weight = 5414.019| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3672 Z= 0.174 Angle : 0.682 10.865 4985 Z= 0.327 Chirality : 0.041 0.164 574 Planarity : 0.004 0.046 611 Dihedral : 5.721 55.056 498 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 6.17 % Allowed : 21.72 % Favored : 72.12 % 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: 1.91 (0.40), residues: 456 helix: 1.98 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.83 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.001 0.000 HIS A 559 PHE 0.054 0.001 PHE A 372 TYR 0.018 0.002 TYR A 215 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6504 (ptp-170) REVERT: A 200 TRP cc_start: 0.9189 (t60) cc_final: 0.8487 (t60) REVERT: A 213 ILE cc_start: 0.9368 (mm) cc_final: 0.9168 (tp) REVERT: A 220 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7390 (m) REVERT: A 307 PHE cc_start: 0.3932 (OUTLIER) cc_final: 0.3631 (m-80) REVERT: A 331 TYR cc_start: 0.9020 (t80) cc_final: 0.8699 (t80) REVERT: A 432 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7610 (mm-30) REVERT: A 474 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8269 (mt-10) REVERT: A 535 TYR cc_start: 0.8806 (t80) cc_final: 0.8477 (t80) outliers start: 23 outliers final: 10 residues processed: 116 average time/residue: 0.1191 time to fit residues: 17.9280 Evaluate side-chains 105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081213 restraints weight = 13790.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.083369 restraints weight = 7851.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084879 restraints weight = 5327.731| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3672 Z= 0.185 Angle : 0.724 11.231 4985 Z= 0.340 Chirality : 0.041 0.178 574 Planarity : 0.005 0.045 611 Dihedral : 5.807 55.798 498 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.70 % Allowed : 23.32 % Favored : 69.97 % 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: 1.87 (0.40), residues: 456 helix: 1.97 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -2.10 (0.66), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.001 0.000 HIS A 303 PHE 0.051 0.002 PHE A 372 TYR 0.017 0.001 TYR A 444 ARG 0.002 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6522 (ptp-170) REVERT: A 200 TRP cc_start: 0.9198 (t60) cc_final: 0.8449 (t60) REVERT: A 331 TYR cc_start: 0.9059 (t80) cc_final: 0.8694 (t80) REVERT: A 432 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 457 GLN cc_start: 0.8332 (pm20) cc_final: 0.8079 (pm20) REVERT: A 458 TYR cc_start: 0.8948 (m-80) cc_final: 0.8730 (m-80) REVERT: A 474 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 535 TYR cc_start: 0.8864 (t80) cc_final: 0.8592 (t80) outliers start: 25 outliers final: 15 residues processed: 109 average time/residue: 0.1148 time to fit residues: 16.3865 Evaluate side-chains 106 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.0170 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.095434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081201 restraints weight = 13878.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.083488 restraints weight = 7946.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.085022 restraints weight = 5305.824| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3672 Z= 0.174 Angle : 0.704 11.746 4985 Z= 0.335 Chirality : 0.040 0.165 574 Planarity : 0.004 0.045 611 Dihedral : 5.832 56.474 498 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.09 % Allowed : 24.13 % Favored : 70.78 % 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: 1.99 (0.41), residues: 456 helix: 2.07 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -2.00 (0.66), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.001 0.000 HIS A 303 PHE 0.056 0.002 PHE A 372 TYR 0.013 0.001 TYR A 477 ARG 0.004 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6508 (ptp-170) REVERT: A 200 TRP cc_start: 0.9190 (t60) cc_final: 0.8452 (t60) REVERT: A 331 TYR cc_start: 0.9073 (t80) cc_final: 0.8730 (t80) REVERT: A 432 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7830 (mm-30) REVERT: A 535 TYR cc_start: 0.8853 (t80) cc_final: 0.8587 (t80) outliers start: 19 outliers final: 12 residues processed: 107 average time/residue: 0.1149 time to fit residues: 16.2837 Evaluate side-chains 105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.093310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079991 restraints weight = 13920.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.082208 restraints weight = 7910.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083662 restraints weight = 5229.738| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3672 Z= 0.250 Angle : 0.805 13.880 4985 Z= 0.374 Chirality : 0.042 0.152 574 Planarity : 0.004 0.046 611 Dihedral : 5.522 59.665 496 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.83 % Allowed : 26.54 % Favored : 68.63 % 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: 1.93 (0.41), residues: 456 helix: 2.03 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.24 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 94 HIS 0.001 0.000 HIS A 303 PHE 0.050 0.002 PHE A 372 TYR 0.014 0.001 TYR A 477 ARG 0.006 0.001 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.407 Fit side-chains REVERT: A 33 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6357 (ptp-170) REVERT: A 200 TRP cc_start: 0.9225 (t60) cc_final: 0.8484 (t60) REVERT: A 457 GLN cc_start: 0.8092 (pm20) cc_final: 0.7829 (pm20) REVERT: A 474 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 482 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8206 (ttmt) REVERT: A 535 TYR cc_start: 0.9001 (t80) cc_final: 0.8759 (t80) outliers start: 18 outliers final: 12 residues processed: 106 average time/residue: 0.1156 time to fit residues: 15.9647 Evaluate side-chains 100 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.094413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.080982 restraints weight = 13448.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.083124 restraints weight = 7819.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.084575 restraints weight = 5261.886| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.191 Angle : 0.833 13.060 4985 Z= 0.374 Chirality : 0.044 0.355 574 Planarity : 0.004 0.047 611 Dihedral : 5.487 59.633 496 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.22 % Allowed : 29.22 % Favored : 67.56 % 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: 1.87 (0.41), residues: 456 helix: 1.97 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.19 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 332 HIS 0.001 0.000 HIS A 521 PHE 0.048 0.002 PHE A 372 TYR 0.017 0.001 TYR A 215 ARG 0.005 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.508 Fit side-chains REVERT: A 33 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6784 (mtt180) REVERT: A 200 TRP cc_start: 0.9135 (t60) cc_final: 0.8490 (t60) REVERT: A 371 MET cc_start: 0.8898 (ptp) cc_final: 0.8560 (mpp) REVERT: A 474 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 535 TYR cc_start: 0.8925 (t80) cc_final: 0.8685 (t80) outliers start: 12 outliers final: 10 residues processed: 99 average time/residue: 0.1173 time to fit residues: 15.2635 Evaluate side-chains 98 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.094679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080466 restraints weight = 13379.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.082713 restraints weight = 7788.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.084232 restraints weight = 5227.012| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3672 Z= 0.204 Angle : 0.852 12.687 4985 Z= 0.383 Chirality : 0.044 0.332 574 Planarity : 0.004 0.046 611 Dihedral : 4.947 54.566 496 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.29 % Allowed : 27.88 % Favored : 67.83 % 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: 1.79 (0.41), residues: 456 helix: 1.92 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -2.03 (0.67), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 517 HIS 0.001 0.000 HIS A 521 PHE 0.044 0.002 PHE A 372 TYR 0.018 0.001 TYR A 477 ARG 0.005 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6372 (ptp-170) REVERT: A 200 TRP cc_start: 0.9132 (t60) cc_final: 0.8489 (t60) REVERT: A 371 MET cc_start: 0.8882 (ptp) cc_final: 0.8544 (mpp) REVERT: A 474 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8246 (mt-10) REVERT: A 504 SER cc_start: 0.9394 (t) cc_final: 0.9185 (p) outliers start: 16 outliers final: 12 residues processed: 107 average time/residue: 0.1126 time to fit residues: 15.9462 Evaluate side-chains 102 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.095379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.081084 restraints weight = 13406.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083288 restraints weight = 7771.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.084843 restraints weight = 5229.102| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3672 Z= 0.201 Angle : 0.879 12.036 4985 Z= 0.400 Chirality : 0.045 0.323 574 Planarity : 0.004 0.044 611 Dihedral : 4.790 54.405 495 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.49 % Allowed : 28.95 % Favored : 67.56 % 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: 1.72 (0.41), residues: 456 helix: 1.87 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -2.04 (0.66), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 517 HIS 0.001 0.000 HIS A 521 PHE 0.051 0.002 PHE A 372 TYR 0.019 0.001 TYR A 215 ARG 0.005 0.000 ARG A 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6790 (mtt180) REVERT: A 200 TRP cc_start: 0.9120 (t60) cc_final: 0.8502 (t60) REVERT: A 371 MET cc_start: 0.8848 (ptp) cc_final: 0.8542 (mpp) REVERT: A 489 MET cc_start: 0.9320 (tpp) cc_final: 0.9100 (tpp) REVERT: A 504 SER cc_start: 0.9374 (t) cc_final: 0.9167 (p) outliers start: 13 outliers final: 11 residues processed: 102 average time/residue: 0.1145 time to fit residues: 15.3033 Evaluate side-chains 102 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 454 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 = 0.3804 r_free = 0.3804 target = 0.095096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.080993 restraints weight = 13675.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.083194 restraints weight = 7825.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.084685 restraints weight = 5245.081| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3672 Z= 0.214 Angle : 0.885 11.952 4985 Z= 0.408 Chirality : 0.045 0.306 574 Planarity : 0.004 0.044 611 Dihedral : 4.838 54.435 495 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.49 % Allowed : 29.76 % Favored : 66.76 % 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: 1.71 (0.41), residues: 456 helix: 1.86 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -2.04 (0.67), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 517 HIS 0.001 0.000 HIS A 521 PHE 0.057 0.002 PHE A 372 TYR 0.016 0.001 TYR A 477 ARG 0.005 0.000 ARG A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.32 seconds wall clock time: 25 minutes 51.60 seconds (1551.60 seconds total)