Starting phenix.real_space_refine on Wed Mar 5 21:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsn_18637/03_2025/8qsn_18637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsn_18637/03_2025/8qsn_18637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsn_18637/03_2025/8qsn_18637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsn_18637/03_2025/8qsn_18637.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsn_18637/03_2025/8qsn_18637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsn_18637/03_2025/8qsn_18637.cif" } resolution = 3.54 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): 0.03s 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: 4.44, per 1000 atoms: 1.24 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: 1.05 Conformation dependent library (CDL) restraints added in 545.2 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: 0.35 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: 1.05 Time building geometry restraints manager: 1.24 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: 0.960 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.360 Find NCS groups from input model: 0.040 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6367 (mtm-85) REVERT: A 44 GLU cc_start: 0.9074 (tp30) cc_final: 0.8872 (tp30) REVERT: A 47 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8533 (tm-30) REVERT: A 91 PHE cc_start: 0.8834 (m-80) cc_final: 0.8615 (m-10) REVERT: A 198 PHE cc_start: 0.9062 (t80) cc_final: 0.8784 (t80) REVERT: A 200 TRP cc_start: 0.9108 (t60) cc_final: 0.8457 (t60) REVERT: A 313 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 342 TYR cc_start: 0.8828 (m-10) cc_final: 0.8493 (m-80) REVERT: A 369 LEU cc_start: 0.8668 (mt) cc_final: 0.8262 (mt) REVERT: A 427 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 451 LEU cc_start: 0.9283 (tp) cc_final: 0.9027 (mp) REVERT: A 454 GLN cc_start: 0.8598 (tp40) cc_final: 0.8199 (tp40) REVERT: A 457 GLN cc_start: 0.7851 (pt0) cc_final: 0.6235 (pt0) REVERT: A 474 GLU cc_start: 0.8866 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 535 TYR cc_start: 0.8685 (t80) cc_final: 0.8193 (t80) outliers start: 14 outliers final: 3 residues processed: 181 average time/residue: 0.1781 time to fit residues: 38.6841 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 : 0.399 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 = 0.3900 r_free = 0.3900 target = 0.098020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.084244 restraints weight = 13317.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.086517 restraints weight = 7613.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.088085 restraints weight = 5076.741| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3672 Z= 0.209 Angle : 0.721 10.088 4985 Z= 0.340 Chirality : 0.040 0.157 574 Planarity : 0.005 0.051 611 Dihedral : 5.720 54.712 502 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.49 % Allowed : 18.77 % Favored : 77.75 % 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: 2.36 (0.40), residues: 456 helix: 2.37 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -1.82 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 69 HIS 0.003 0.001 HIS A 521 PHE 0.036 0.002 PHE A 417 TYR 0.013 0.002 TYR A 477 ARG 0.005 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 122 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6552 (ptp-170) REVERT: A 44 GLU cc_start: 0.9325 (tp30) cc_final: 0.9071 (tp30) REVERT: A 47 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 91 PHE cc_start: 0.8886 (m-80) cc_final: 0.8645 (m-10) REVERT: A 200 TRP cc_start: 0.9091 (t60) cc_final: 0.8394 (t60) REVERT: A 235 LEU cc_start: 0.9524 (mt) cc_final: 0.8957 (tp) REVERT: A 301 MET cc_start: 0.5936 (tpt) cc_final: 0.5695 (tmm) REVERT: A 309 GLU cc_start: 0.8846 (pm20) cc_final: 0.8263 (pm20) REVERT: A 331 TYR cc_start: 0.9032 (t80) cc_final: 0.8524 (t80) REVERT: A 427 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 451 LEU cc_start: 0.9285 (tp) cc_final: 0.9017 (mp) REVERT: A 465 GLU cc_start: 0.8442 (tp30) cc_final: 0.8229 (tp30) REVERT: A 535 TYR cc_start: 0.8827 (t80) cc_final: 0.8374 (t80) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.1118 time to fit residues: 17.4584 Evaluate side-chains 105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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: 7.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.096254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.082680 restraints weight = 13785.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.084845 restraints weight = 7921.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086127 restraints weight = 5364.996| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3672 Z= 0.208 Angle : 0.706 11.290 4985 Z= 0.332 Chirality : 0.040 0.156 574 Planarity : 0.005 0.056 611 Dihedral : 5.770 54.705 500 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.36 % Allowed : 19.84 % Favored : 74.80 % 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: 2.16 (0.40), residues: 456 helix: 2.16 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.84 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 69 HIS 0.002 0.000 HIS A 521 PHE 0.046 0.002 PHE A 372 TYR 0.017 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 123 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6545 (ptp-170) REVERT: A 200 TRP cc_start: 0.9139 (t60) cc_final: 0.8471 (t60) REVERT: A 213 ILE cc_start: 0.9474 (mm) cc_final: 0.9259 (tp) REVERT: A 301 MET cc_start: 0.6217 (tpt) cc_final: 0.5947 (tmm) REVERT: A 307 PHE cc_start: 0.3857 (OUTLIER) cc_final: 0.3556 (m-80) REVERT: A 331 TYR cc_start: 0.9104 (t80) cc_final: 0.8678 (t80) REVERT: A 413 MET cc_start: 0.8874 (tmm) cc_final: 0.8624 (tmm) REVERT: A 427 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8602 (mt) REVERT: A 458 TYR cc_start: 0.8959 (m-80) cc_final: 0.8726 (m-80) REVERT: A 474 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 489 MET cc_start: 0.9539 (tpp) cc_final: 0.9321 (tpp) REVERT: A 535 TYR cc_start: 0.8933 (t80) cc_final: 0.8548 (t80) outliers start: 20 outliers final: 10 residues processed: 117 average time/residue: 0.1107 time to fit residues: 17.1045 Evaluate side-chains 107 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 427 LEU Chi-restraints excluded: chain A residue 429 LEU 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: 0.8980 chunk 42 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 559 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.097267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.083874 restraints weight = 13784.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.086094 restraints weight = 7935.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.087565 restraints weight = 5319.578| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3672 Z= 0.178 Angle : 0.667 10.727 4985 Z= 0.323 Chirality : 0.040 0.171 574 Planarity : 0.005 0.046 611 Dihedral : 5.923 54.742 500 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.90 % Allowed : 23.32 % 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: 2.00 (0.40), residues: 456 helix: 2.03 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.74 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.001 0.000 HIS A 559 PHE 0.057 0.001 PHE A 372 TYR 0.019 0.002 TYR A 215 ARG 0.004 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 123 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6561 (ptp-170) REVERT: A 200 TRP cc_start: 0.9168 (t60) cc_final: 0.8465 (t60) REVERT: A 213 ILE cc_start: 0.9465 (mm) cc_final: 0.9256 (tp) REVERT: A 307 PHE cc_start: 0.3846 (OUTLIER) cc_final: 0.3520 (m-80) REVERT: A 310 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 331 TYR cc_start: 0.9116 (t80) cc_final: 0.8717 (t80) REVERT: A 427 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8608 (mt) REVERT: A 432 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 451 LEU cc_start: 0.9251 (tp) cc_final: 0.9035 (mp) REVERT: A 458 TYR cc_start: 0.8976 (m-80) cc_final: 0.8765 (m-80) REVERT: A 474 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 535 TYR cc_start: 0.8894 (t80) cc_final: 0.8530 (t80) outliers start: 22 outliers final: 10 residues processed: 117 average time/residue: 0.1147 time to fit residues: 17.4656 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 : 0.373 ------------------------------------------------------------------------------- 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 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 427 LEU 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: 0.0270 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.095423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.081779 restraints weight = 14003.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.084082 restraints weight = 7904.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.085576 restraints weight = 5232.467| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3672 Z= 0.171 Angle : 0.719 13.254 4985 Z= 0.331 Chirality : 0.041 0.186 574 Planarity : 0.005 0.045 611 Dihedral : 5.972 55.011 500 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.90 % Allowed : 25.20 % Favored : 68.90 % 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: 1.90 (0.40), residues: 456 helix: 1.98 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.84 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 368 HIS 0.001 0.000 HIS A 303 PHE 0.055 0.002 PHE A 372 TYR 0.017 0.001 TYR A 444 ARG 0.003 0.000 ARG A 48 *********************** 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 124 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6501 (ptp-170) REVERT: A 44 GLU cc_start: 0.9166 (tp30) cc_final: 0.8793 (tp30) REVERT: A 200 TRP cc_start: 0.9176 (t60) cc_final: 0.8481 (t60) REVERT: A 213 ILE cc_start: 0.9441 (mm) cc_final: 0.9224 (tp) REVERT: A 331 TYR cc_start: 0.9115 (t80) cc_final: 0.8690 (t80) REVERT: A 371 MET cc_start: 0.8809 (mtt) cc_final: 0.8603 (ptp) REVERT: A 427 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8565 (mt) REVERT: A 432 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 458 TYR cc_start: 0.8902 (m-80) cc_final: 0.8692 (m-80) REVERT: A 474 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 535 TYR cc_start: 0.8873 (t80) cc_final: 0.8515 (t80) outliers start: 22 outliers final: 10 residues processed: 116 average time/residue: 0.1182 time to fit residues: 17.7642 Evaluate side-chains 110 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.095528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.082367 restraints weight = 14006.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.084534 restraints weight = 8004.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086009 restraints weight = 5358.578| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5122 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= 0.191 Angle : 0.743 14.039 4985 Z= 0.342 Chirality : 0.040 0.171 574 Planarity : 0.004 0.046 611 Dihedral : 6.039 56.461 500 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.36 % Allowed : 25.47 % Favored : 69.17 % 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: 1.96 (0.40), residues: 456 helix: 2.04 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.96 (0.66), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.001 0.000 HIS A 348 PHE 0.051 0.001 PHE A 372 TYR 0.014 0.001 TYR A 215 ARG 0.005 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 117 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6461 (ptp-170) REVERT: A 200 TRP cc_start: 0.9170 (t60) cc_final: 0.8421 (t60) REVERT: A 213 ILE cc_start: 0.9424 (mm) cc_final: 0.9214 (tp) REVERT: A 331 TYR cc_start: 0.9143 (t80) cc_final: 0.8699 (t80) REVERT: A 427 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8648 (mt) REVERT: A 432 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 474 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 535 TYR cc_start: 0.8940 (t80) cc_final: 0.8615 (t80) outliers start: 20 outliers final: 11 residues processed: 111 average time/residue: 0.1117 time to fit residues: 16.2100 Evaluate side-chains 103 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 207 ILE 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 427 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.095218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.081227 restraints weight = 13831.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.083475 restraints weight = 7831.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.084982 restraints weight = 5173.578| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3672 Z= 0.222 Angle : 0.807 13.987 4985 Z= 0.366 Chirality : 0.042 0.163 574 Planarity : 0.004 0.045 611 Dihedral : 5.695 59.727 498 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.83 % Allowed : 28.15 % Favored : 67.02 % 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: 1.86 (0.41), residues: 456 helix: 1.96 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.96 (0.66), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 453 HIS 0.001 0.000 HIS A 559 PHE 0.053 0.002 PHE A 372 TYR 0.014 0.001 TYR A 477 ARG 0.004 0.000 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 117 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.429 Fit side-chains REVERT: A 33 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6471 (ptp-170) REVERT: A 200 TRP cc_start: 0.9186 (t60) cc_final: 0.8453 (t60) REVERT: A 310 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7082 (tm-30) REVERT: A 427 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8647 (mt) REVERT: A 432 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 474 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 535 TYR cc_start: 0.8978 (t80) cc_final: 0.8740 (t80) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.1140 time to fit residues: 16.4597 Evaluate side-chains 101 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 191 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 427 LEU Chi-restraints excluded: chain A residue 429 LEU 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: 0.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.0670 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.096974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.083234 restraints weight = 13720.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.085545 restraints weight = 7801.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.087118 restraints weight = 5162.831| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5601 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= 0.192 Angle : 0.861 16.434 4985 Z= 0.385 Chirality : 0.044 0.337 574 Planarity : 0.004 0.041 611 Dihedral : 5.672 58.860 498 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: 1.63 (0.40), residues: 456 helix: 1.78 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.12 (0.68), residues: 85 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 0.056 0.002 PHE A 372 TYR 0.018 0.001 TYR A 215 ARG 0.006 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 114 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6467 (ptp-170) REVERT: A 200 TRP cc_start: 0.9102 (t60) cc_final: 0.8463 (t60) REVERT: A 331 TYR cc_start: 0.9122 (t80) cc_final: 0.8682 (t80) REVERT: A 371 MET cc_start: 0.8774 (ptp) cc_final: 0.8467 (mpp) REVERT: A 427 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8591 (mt) REVERT: A 432 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 474 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8203 (mt-10) REVERT: A 504 SER cc_start: 0.9416 (t) cc_final: 0.9192 (p) REVERT: A 535 TYR cc_start: 0.8920 (t80) cc_final: 0.8695 (t80) outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.1192 time to fit residues: 17.2377 Evaluate side-chains 105 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 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 427 LEU Chi-restraints excluded: chain A residue 429 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: 0.6980 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.097124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.082795 restraints weight = 13524.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.085127 restraints weight = 7821.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.086674 restraints weight = 5252.267| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5820 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= 0.206 Angle : 0.865 12.954 4985 Z= 0.390 Chirality : 0.044 0.320 574 Planarity : 0.004 0.040 611 Dihedral : 5.210 54.384 498 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.75 % Allowed : 27.88 % Favored : 68.36 % 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: 1.85 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.98 (0.67), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS A 395 PHE 0.051 0.002 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.006 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 112 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.394 Fit side-chains REVERT: A 33 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6473 (ptp-170) REVERT: A 172 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8893 (mmmt) REVERT: A 200 TRP cc_start: 0.9099 (t60) cc_final: 0.8465 (t60) REVERT: A 331 TYR cc_start: 0.9118 (t80) cc_final: 0.8690 (t80) REVERT: A 371 MET cc_start: 0.8777 (ptp) cc_final: 0.8479 (mpp) REVERT: A 474 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8160 (mt-10) REVERT: A 504 SER cc_start: 0.9421 (t) cc_final: 0.9194 (p) REVERT: A 535 TYR cc_start: 0.8944 (t80) cc_final: 0.8721 (t80) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.1116 time to fit residues: 15.6045 Evaluate side-chains 103 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.097531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.082979 restraints weight = 13542.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.085278 restraints weight = 7864.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.086851 restraints weight = 5295.127| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3672 Z= 0.213 Angle : 0.891 14.616 4985 Z= 0.406 Chirality : 0.046 0.315 574 Planarity : 0.004 0.040 611 Dihedral : 4.808 54.339 495 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.68 % Allowed : 29.76 % 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: 1.55 (0.40), residues: 456 helix: 1.75 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -2.34 (0.68), residues: 84 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 0.049 0.001 PHE A 372 TYR 0.019 0.001 TYR A 215 ARG 0.006 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: 10 poor density : 96 time to evaluate : 0.377 Fit side-chains REVERT: A 33 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6408 (ptp-170) REVERT: A 200 TRP cc_start: 0.9093 (t60) cc_final: 0.8488 (t60) REVERT: A 331 TYR cc_start: 0.9094 (t80) cc_final: 0.8664 (t80) REVERT: A 371 MET cc_start: 0.8737 (ptp) cc_final: 0.8469 (mpp) REVERT: A 474 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8169 (mt-10) REVERT: A 489 MET cc_start: 0.9289 (tpp) cc_final: 0.9070 (tpp) REVERT: A 493 PHE cc_start: 0.9471 (m-80) cc_final: 0.9267 (m-80) REVERT: A 504 SER cc_start: 0.9430 (t) cc_final: 0.9217 (p) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1184 time to fit residues: 15.9195 Evaluate side-chains 102 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 258 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.097232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.083891 restraints weight = 13769.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.086148 restraints weight = 7794.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.087672 restraints weight = 5180.318| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3672 Z= 0.216 Angle : 0.900 12.774 4985 Z= 0.413 Chirality : 0.046 0.283 574 Planarity : 0.004 0.039 611 Dihedral : 4.860 54.186 495 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.68 % Allowed : 30.56 % 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: 1.54 (0.41), residues: 456 helix: 1.74 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -2.34 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 517 HIS 0.001 0.000 HIS A 521 PHE 0.055 0.002 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.007 0.001 ARG A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.14 seconds wall clock time: 26 minutes 28.94 seconds (1588.94 seconds total)