Starting phenix.real_space_refine on Wed Mar 4 03:23:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmy_13544/03_2026/7pmy_13544.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmy_13544/03_2026/7pmy_13544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmy_13544/03_2026/7pmy_13544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmy_13544/03_2026/7pmy_13544.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmy_13544/03_2026/7pmy_13544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmy_13544/03_2026/7pmy_13544.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 3425 2.51 5 N 845 2.21 5 O 924 1.98 5 H 5276 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10499 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10466 Classifications: {'peptide': 657} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 632} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.19 Number of scatterers: 10499 At special positions: 0 Unit cell: (85.85, 82.45, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 924 8.00 N 845 7.00 C 3425 6.00 H 5276 1.00 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: 0.79 Conformation dependent library (CDL) restraints added in 365.2 milliseconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1238 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 62.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.142A pdb=" N ILE A 46 " --> pdb=" O TYR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 66 removed outlier: 3.630A pdb=" N VAL A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 78 through 95 Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.073A pdb=" N TRP A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.706A pdb=" N GLY A 137 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 171 removed outlier: 3.988A pdb=" N VAL A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.627A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 208 Proline residue: A 203 - end of helix removed outlier: 3.828A pdb=" N GLY A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 4.082A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Proline residue: A 224 - end of helix removed outlier: 3.750A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 249 through 270 removed outlier: 4.671A pdb=" N ALA A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.734A pdb=" N TRP A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.629A pdb=" N VAL A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Proline residue: A 308 - end of helix No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.754A pdb=" N TRP A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 4.706A pdb=" N THR A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.521A pdb=" N ILE A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 357 - end of helix removed outlier: 7.533A pdb=" N ASP A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 376 removed outlier: 4.149A pdb=" N SER A 376 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 405 removed outlier: 3.631A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'A' and resid 611 through 637 removed outlier: 3.762A pdb=" N TYR A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 667 removed outlier: 3.763A pdb=" N LEU A 645 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 removed outlier: 3.617A pdb=" N ILE A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443 removed outlier: 3.605A pdb=" N LEU A 439 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545 removed outlier: 6.558A pdb=" N THR A 516 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE A 583 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 518 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 585 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 520 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ASN A 587 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 580 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 539 removed outlier: 4.031A pdb=" N HIS A 560 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 333 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5265 1.03 - 1.23: 11 1.23 - 1.42: 2276 1.42 - 1.61: 3032 1.61 - 1.81: 47 Bond restraints: 10631 Sorted by residual: bond pdb=" N ASN A 41 " pdb=" CA ASN A 41 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N ASN A 41 " pdb=" H ASN A 41 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" CA VAL A 430 " pdb=" CB VAL A 430 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.02e+00 bond pdb=" CA HIS A 176 " pdb=" C HIS A 176 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 7.14e-01 bond pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.08e-01 ... (remaining 10626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 17586 0.92 - 1.84: 1551 1.84 - 2.76: 57 2.76 - 3.69: 16 3.69 - 4.61: 11 Bond angle restraints: 19221 Sorted by residual: angle pdb=" N ILE A 354 " pdb=" CA ILE A 354 " pdb=" C ILE A 354 " ideal model delta sigma weight residual 112.96 109.35 3.61 1.00e+00 1.00e+00 1.31e+01 angle pdb=" N HIS A 524 " pdb=" CA HIS A 524 " pdb=" C HIS A 524 " ideal model delta sigma weight residual 112.93 110.07 2.86 1.12e+00 7.97e-01 6.54e+00 angle pdb=" N SER A 640 " pdb=" CA SER A 640 " pdb=" CB SER A 640 " ideal model delta sigma weight residual 113.65 110.20 3.45 1.47e+00 4.63e-01 5.51e+00 angle pdb=" N ARG A 509 " pdb=" CA ARG A 509 " pdb=" C ARG A 509 " ideal model delta sigma weight residual 114.56 111.70 2.86 1.27e+00 6.20e-01 5.06e+00 angle pdb=" C PHE A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta sigma weight residual 122.97 120.99 1.98 9.80e-01 1.04e+00 4.10e+00 ... (remaining 19216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 4663 15.36 - 30.72: 212 30.72 - 46.09: 73 46.09 - 61.45: 63 61.45 - 76.81: 4 Dihedral angle restraints: 5015 sinusoidal: 2646 harmonic: 2369 Sorted by residual: dihedral pdb=" CA LYS A 244 " pdb=" CB LYS A 244 " pdb=" CG LYS A 244 " pdb=" CD LYS A 244 " ideal model delta sinusoidal sigma weight residual 180.00 -120.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU A 309 " pdb=" C LEU A 309 " pdb=" N PRO A 310 " pdb=" CA PRO A 310 " ideal model delta harmonic sigma weight residual -180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" N HIS A 125 " pdb=" CA HIS A 125 " pdb=" CB HIS A 125 " pdb=" CG HIS A 125 " ideal model delta sinusoidal sigma weight residual -180.00 -127.17 -52.83 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 5012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 578 0.029 - 0.058: 159 0.058 - 0.088: 59 0.088 - 0.117: 32 0.117 - 0.146: 4 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ILE A 356 " pdb=" N ILE A 356 " pdb=" C ILE A 356 " pdb=" CB ILE A 356 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE A 598 " pdb=" N ILE A 598 " pdb=" C ILE A 598 " pdb=" CB ILE A 598 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE A 601 " pdb=" N ILE A 601 " pdb=" C ILE A 601 " pdb=" CB ILE A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 829 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 601 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 602 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 307 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 308 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 309 " -0.016 5.00e-02 4.00e+02 2.37e-02 8.95e-01 pdb=" N PRO A 310 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " -0.013 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 885 2.23 - 2.82: 23188 2.82 - 3.41: 28626 3.41 - 4.01: 37576 4.01 - 4.60: 57865 Nonbonded interactions: 148140 Sorted by model distance: nonbonded pdb=" OE2 GLU A 507 " pdb=" H THR A 510 " model vdw 1.631 2.450 nonbonded pdb=" H GLN A 412 " pdb=" OE1 GLU A 483 " model vdw 1.640 2.450 nonbonded pdb=" HE ARG A 266 " pdb=" OE1 GLN A 278 " model vdw 1.654 2.450 nonbonded pdb=" OD2 ASP A 317 " pdb="HD22 ASN A 657 " model vdw 1.655 2.450 nonbonded pdb="HH22 ARG A 277 " pdb=" OE2 GLU A 286 " model vdw 1.659 2.450 ... (remaining 148135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.540 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: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.560 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 0.033 5355 Z= 0.111 Angle : 0.460 4.606 7278 Z= 0.276 Chirality : 0.036 0.146 832 Planarity : 0.003 0.031 906 Dihedral : 9.150 67.769 1896 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.98 % Favored : 97.86 % Rotamer: Outliers : 1.40 % Allowed : 3.51 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.33), residues: 655 helix: 0.76 (0.29), residues: 336 sheet: 0.40 (0.51), residues: 104 loop : -0.08 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.010 0.001 TYR A 121 PHE 0.007 0.001 PHE A 172 TRP 0.004 0.001 TRP A 313 HIS 0.001 0.000 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 5355) covalent geometry : angle 0.46032 ( 7278) hydrogen bonds : bond 0.26361 ( 329) hydrogen bonds : angle 8.70820 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9282 (tp) cc_final: 0.8998 (tt) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.1697 time to fit residues: 19.9195 Evaluate side-chains 67 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 ASN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.134559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099236 restraints weight = 31501.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099584 restraints weight = 31372.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101177 restraints weight = 26624.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101040 restraints weight = 18638.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101436 restraints weight = 19830.215| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5355 Z= 0.161 Angle : 0.573 5.300 7278 Z= 0.318 Chirality : 0.040 0.142 832 Planarity : 0.005 0.065 906 Dihedral : 6.058 58.877 718 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.21 % Favored : 96.64 % Rotamer: Outliers : 1.75 % Allowed : 7.02 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.32), residues: 655 helix: 1.09 (0.27), residues: 347 sheet: 0.04 (0.52), residues: 93 loop : -0.83 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 518 TYR 0.022 0.001 TYR A 121 PHE 0.014 0.001 PHE A 391 TRP 0.016 0.001 TRP A 596 HIS 0.002 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5355) covalent geometry : angle 0.57263 ( 7278) hydrogen bonds : bond 0.06962 ( 329) hydrogen bonds : angle 6.23743 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9130 (tp) cc_final: 0.8851 (tt) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.1494 time to fit residues: 14.9080 Evaluate side-chains 64 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.130427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095676 restraints weight = 32149.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093645 restraints weight = 33019.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095627 restraints weight = 31681.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095675 restraints weight = 20557.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096496 restraints weight = 19480.189| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 5355 Z= 0.346 Angle : 0.623 5.167 7278 Z= 0.352 Chirality : 0.043 0.156 832 Planarity : 0.005 0.056 906 Dihedral : 6.237 57.200 718 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.93 % Allowed : 8.60 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.32), residues: 655 helix: 0.62 (0.27), residues: 344 sheet: -0.19 (0.53), residues: 93 loop : -1.11 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 332 TYR 0.027 0.002 TYR A 121 PHE 0.016 0.002 PHE A 261 TRP 0.009 0.001 TRP A 280 HIS 0.003 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00786 ( 5355) covalent geometry : angle 0.62298 ( 7278) hydrogen bonds : bond 0.06375 ( 329) hydrogen bonds : angle 6.10214 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9124 (tp) cc_final: 0.8811 (tt) outliers start: 11 outliers final: 11 residues processed: 67 average time/residue: 0.1533 time to fit residues: 13.7880 Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 53 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 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 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099753 restraints weight = 32015.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098145 restraints weight = 32325.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099920 restraints weight = 27133.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100012 restraints weight = 19661.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100397 restraints weight = 20783.400| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5355 Z= 0.128 Angle : 0.512 4.656 7278 Z= 0.278 Chirality : 0.039 0.141 832 Planarity : 0.004 0.051 906 Dihedral : 6.072 58.865 718 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.75 % Allowed : 8.77 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.32), residues: 655 helix: 1.05 (0.27), residues: 341 sheet: -0.24 (0.51), residues: 93 loop : -1.17 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.017 0.001 TYR A 121 PHE 0.017 0.001 PHE A 261 TRP 0.016 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5355) covalent geometry : angle 0.51179 ( 7278) hydrogen bonds : bond 0.05212 ( 329) hydrogen bonds : angle 5.47520 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 PHE cc_start: 0.6057 (m-80) cc_final: 0.5840 (m-80) REVERT: A 582 LEU cc_start: 0.9116 (tp) cc_final: 0.8795 (tt) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.1545 time to fit residues: 13.0548 Evaluate side-chains 60 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.133923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099363 restraints weight = 31875.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098303 restraints weight = 27083.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099902 restraints weight = 23147.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.099930 restraints weight = 17200.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100204 restraints weight = 19488.523| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5355 Z= 0.150 Angle : 0.504 6.263 7278 Z= 0.274 Chirality : 0.039 0.140 832 Planarity : 0.004 0.047 906 Dihedral : 5.902 58.780 717 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.58 % Allowed : 9.65 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.32), residues: 655 helix: 1.12 (0.28), residues: 341 sheet: -0.24 (0.50), residues: 93 loop : -1.16 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 322 TYR 0.020 0.001 TYR A 121 PHE 0.016 0.001 PHE A 261 TRP 0.016 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5355) covalent geometry : angle 0.50414 ( 7278) hydrogen bonds : bond 0.04850 ( 329) hydrogen bonds : angle 5.30220 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9134 (tp) cc_final: 0.8834 (tt) outliers start: 9 outliers final: 9 residues processed: 61 average time/residue: 0.1548 time to fit residues: 12.5637 Evaluate side-chains 59 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.138389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.100552 restraints weight = 33097.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100000 restraints weight = 21754.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101457 restraints weight = 20644.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.102007 restraints weight = 13022.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.102824 restraints weight = 11967.469| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5355 Z= 0.177 Angle : 0.523 6.827 7278 Z= 0.285 Chirality : 0.039 0.142 832 Planarity : 0.004 0.046 906 Dihedral : 5.903 58.493 717 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.75 % Allowed : 10.70 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.32), residues: 655 helix: 1.11 (0.28), residues: 344 sheet: -0.28 (0.50), residues: 93 loop : -1.07 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.021 0.001 TYR A 121 PHE 0.016 0.001 PHE A 261 TRP 0.013 0.001 TRP A 596 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5355) covalent geometry : angle 0.52319 ( 7278) hydrogen bonds : bond 0.04719 ( 329) hydrogen bonds : angle 5.25312 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9412 (tp) cc_final: 0.9161 (tt) outliers start: 10 outliers final: 10 residues processed: 60 average time/residue: 0.1522 time to fit residues: 12.3247 Evaluate side-chains 60 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 43 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.139006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102590 restraints weight = 33953.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.101740 restraints weight = 24024.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102977 restraints weight = 21051.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104222 restraints weight = 13857.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104597 restraints weight = 12307.036| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5355 Z= 0.178 Angle : 0.520 6.000 7278 Z= 0.282 Chirality : 0.039 0.174 832 Planarity : 0.004 0.045 906 Dihedral : 5.891 58.181 717 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.93 % Allowed : 10.88 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.32), residues: 655 helix: 1.14 (0.28), residues: 344 sheet: -0.13 (0.50), residues: 93 loop : -1.08 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 492 TYR 0.020 0.001 TYR A 121 PHE 0.016 0.001 PHE A 261 TRP 0.015 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5355) covalent geometry : angle 0.52031 ( 7278) hydrogen bonds : bond 0.04591 ( 329) hydrogen bonds : angle 5.13911 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9390 (tp) cc_final: 0.9133 (tt) outliers start: 11 outliers final: 10 residues processed: 59 average time/residue: 0.1586 time to fit residues: 12.4662 Evaluate side-chains 60 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.0060 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.140384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.104260 restraints weight = 33621.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103709 restraints weight = 22135.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105263 restraints weight = 17249.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105374 restraints weight = 13747.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106632 restraints weight = 13701.941| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5355 Z= 0.114 Angle : 0.491 6.181 7278 Z= 0.261 Chirality : 0.038 0.143 832 Planarity : 0.004 0.043 906 Dihedral : 5.809 59.271 717 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.75 % Allowed : 11.05 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.32), residues: 655 helix: 1.35 (0.28), residues: 341 sheet: 0.09 (0.50), residues: 93 loop : -1.13 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.018 0.001 TYR A 121 PHE 0.016 0.001 PHE A 261 TRP 0.014 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5355) covalent geometry : angle 0.49070 ( 7278) hydrogen bonds : bond 0.04222 ( 329) hydrogen bonds : angle 4.89473 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7808 (tpp-160) REVERT: A 577 PHE cc_start: 0.6252 (m-80) cc_final: 0.5998 (m-80) REVERT: A 582 LEU cc_start: 0.9336 (tp) cc_final: 0.9072 (tt) outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.1436 time to fit residues: 11.9914 Evaluate side-chains 58 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 48 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.140219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104241 restraints weight = 33663.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.103856 restraints weight = 25896.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105472 restraints weight = 23287.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.105952 restraints weight = 14762.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106873 restraints weight = 13678.605| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5355 Z= 0.142 Angle : 0.499 6.730 7278 Z= 0.266 Chirality : 0.038 0.143 832 Planarity : 0.004 0.043 906 Dihedral : 5.791 59.058 717 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.93 % Allowed : 11.75 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.32), residues: 655 helix: 1.33 (0.28), residues: 343 sheet: 0.11 (0.49), residues: 93 loop : -1.09 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 322 TYR 0.021 0.001 TYR A 121 PHE 0.016 0.001 PHE A 261 TRP 0.013 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5355) covalent geometry : angle 0.49927 ( 7278) hydrogen bonds : bond 0.04216 ( 329) hydrogen bonds : angle 4.87538 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7845 (tpp-160) REVERT: A 577 PHE cc_start: 0.6218 (m-80) cc_final: 0.5993 (m-80) REVERT: A 582 LEU cc_start: 0.9284 (tp) cc_final: 0.9018 (tt) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.1490 time to fit residues: 11.7053 Evaluate side-chains 58 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.0570 chunk 38 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.141976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.106299 restraints weight = 33823.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106815 restraints weight = 23367.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108071 restraints weight = 20783.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108643 restraints weight = 12661.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.109178 restraints weight = 11891.194| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5355 Z= 0.104 Angle : 0.489 5.828 7278 Z= 0.256 Chirality : 0.038 0.140 832 Planarity : 0.004 0.042 906 Dihedral : 5.729 59.953 717 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.75 % Allowed : 11.75 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.33), residues: 655 helix: 1.59 (0.28), residues: 338 sheet: 0.33 (0.49), residues: 93 loop : -0.83 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.019 0.001 TYR A 121 PHE 0.017 0.001 PHE A 261 TRP 0.013 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 5355) covalent geometry : angle 0.48861 ( 7278) hydrogen bonds : bond 0.03943 ( 329) hydrogen bonds : angle 4.70183 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 PHE cc_start: 0.6292 (m-80) cc_final: 0.6035 (m-80) outliers start: 10 outliers final: 10 residues processed: 61 average time/residue: 0.1482 time to fit residues: 12.3686 Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.140445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.103620 restraints weight = 32873.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.104260 restraints weight = 25353.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.105819 restraints weight = 20888.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106135 restraints weight = 12645.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106935 restraints weight = 11820.781| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5355 Z= 0.146 Angle : 0.499 7.386 7278 Z= 0.266 Chirality : 0.038 0.142 832 Planarity : 0.004 0.042 906 Dihedral : 5.715 59.373 717 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.93 % Allowed : 11.75 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.33), residues: 655 helix: 1.54 (0.28), residues: 339 sheet: 0.31 (0.50), residues: 93 loop : -0.90 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.021 0.001 TYR A 121 PHE 0.016 0.001 PHE A 261 TRP 0.012 0.001 TRP A 596 HIS 0.002 0.000 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5355) covalent geometry : angle 0.49909 ( 7278) hydrogen bonds : bond 0.04035 ( 329) hydrogen bonds : angle 4.73870 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.67 seconds wall clock time: 31 minutes 46.35 seconds (1906.35 seconds total)