Starting phenix.real_space_refine on Thu Jul 2 00:27:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hez_34705/07_2026/8hez_34705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hez_34705/07_2026/8hez_34705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hez_34705/07_2026/8hez_34705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hez_34705/07_2026/8hez_34705.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hez_34705/07_2026/8hez_34705.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hez_34705/07_2026/8hez_34705.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hez_34705/07_2026/8hez_34705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hez_34705/07_2026/8hez_34705.cif" } resolution = 2.8 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians S 37 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3129 2.51 5 N 769 2.21 5 O 802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4739 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4461 Classifications: {'peptide': 582} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Unusual residues: {' NA': 1, 'LE6': 1, 'NAG': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.21, per 1000 atoms: 0.26 Number of scatterers: 4739 At special positions: 0 Unit cell: (74.1469, 76.3602, 90.7469, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 37 16.00 Na 1 11.00 O 802 8.00 N 769 7.00 C 3129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.08 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.11 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.09 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.01 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 250 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 178.1 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 82.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 22 through 47 removed outlier: 4.000A pdb=" N ILE A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.837A pdb=" N PHE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 3.761A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.056A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.675A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 175 through 192 removed outlier: 4.149A pdb=" N GLY A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 224 removed outlier: 3.630A pdb=" N VAL A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.575A pdb=" N PHE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.403A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.551A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 377 through 409 removed outlier: 3.851A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 420 through 446 removed outlier: 3.609A pdb=" N VAL A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.819A pdb=" N ASP A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 481 through 507 Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 525 through 547 removed outlier: 3.586A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 672 Processing helix chain 'B' and resid 29 through 55 347 hydrogen bonds defined for protein. 1041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 703 1.31 - 1.44: 1405 1.44 - 1.58: 2697 1.58 - 1.71: 0 1.71 - 1.85: 58 Bond restraints: 4863 Sorted by residual: bond pdb=" C THR A 323 " pdb=" O THR A 323 " ideal model delta sigma weight residual 1.243 1.191 0.053 9.50e-03 1.11e+04 3.08e+01 bond pdb=" C PRO A 66 " pdb=" O PRO A 66 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.16e-02 7.43e+03 2.99e+01 bond pdb=" C TYR A 319 " pdb=" O TYR A 319 " ideal model delta sigma weight residual 1.236 1.293 -0.056 1.15e-02 7.56e+03 2.38e+01 bond pdb=" CA SER A 335 " pdb=" CB SER A 335 " ideal model delta sigma weight residual 1.528 1.461 0.068 1.56e-02 4.11e+03 1.90e+01 bond pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta sigma weight residual 1.457 1.505 -0.047 1.10e-02 8.26e+03 1.85e+01 ... (remaining 4858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 4306 2.12 - 4.23: 2000 4.23 - 6.35: 297 6.35 - 8.46: 25 8.46 - 10.58: 6 Bond angle restraints: 6634 Sorted by residual: angle pdb=" CA THR A 119 " pdb=" CB THR A 119 " pdb=" OG1 THR A 119 " ideal model delta sigma weight residual 109.60 120.00 -10.40 1.50e+00 4.44e-01 4.81e+01 angle pdb=" C LEU A 521 " pdb=" N CYS A 522 " pdb=" CA CYS A 522 " ideal model delta sigma weight residual 120.60 130.85 -10.25 1.60e+00 3.91e-01 4.11e+01 angle pdb=" C ALA A 303 " pdb=" N GLY A 304 " pdb=" CA GLY A 304 " ideal model delta sigma weight residual 120.10 126.02 -5.92 9.50e-01 1.11e+00 3.89e+01 angle pdb=" N PRO A 465 " pdb=" CA PRO A 465 " pdb=" C PRO A 465 " ideal model delta sigma weight residual 110.70 117.68 -6.98 1.22e+00 6.72e-01 3.27e+01 angle pdb=" CA LEU A 107 " pdb=" C LEU A 107 " pdb=" O LEU A 107 " ideal model delta sigma weight residual 120.42 114.37 6.05 1.06e+00 8.90e-01 3.26e+01 ... (remaining 6629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.53: 2429 13.53 - 27.05: 262 27.05 - 40.57: 86 40.57 - 54.09: 21 54.09 - 67.62: 9 Dihedral angle restraints: 2807 sinusoidal: 1067 harmonic: 1740 Sorted by residual: dihedral pdb=" CA HIS A 557 " pdb=" C HIS A 557 " pdb=" N ARG A 558 " pdb=" CA ARG A 558 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LYS A 554 " pdb=" C LYS A 554 " pdb=" N HIS A 555 " pdb=" CA HIS A 555 " ideal model delta harmonic sigma weight residual 180.00 152.24 27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLY A 92 " pdb=" C GLY A 92 " pdb=" N LEU A 93 " pdb=" CA LEU A 93 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 2804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 502 0.080 - 0.160: 225 0.160 - 0.240: 43 0.240 - 0.320: 3 0.320 - 0.400: 1 Chirality restraints: 774 Sorted by residual: chirality pdb=" CB VAL A 95 " pdb=" CA VAL A 95 " pdb=" CG1 VAL A 95 " pdb=" CG2 VAL A 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB VAL A 560 " pdb=" CA VAL A 560 " pdb=" CG1 VAL A 560 " pdb=" CG2 VAL A 560 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VAL A 106 " pdb=" CA VAL A 106 " pdb=" CG1 VAL A 106 " pdb=" CG2 VAL A 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 771 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 98 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C PHE A 98 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 98 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 99 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 128 " 0.025 2.00e-02 2.50e+03 1.41e-02 3.95e+00 pdb=" CG TYR A 128 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 128 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 128 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 128 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 128 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 128 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 128 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 300 " -0.034 9.50e-02 1.11e+02 2.18e-02 3.17e+00 pdb=" NE ARG A 300 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 300 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 300 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 300 " 0.009 2.00e-02 2.50e+03 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 85 2.70 - 3.25: 4721 3.25 - 3.80: 7967 3.80 - 4.35: 10735 4.35 - 4.90: 17400 Nonbonded interactions: 40908 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 803 " model vdw 2.144 2.470 nonbonded pdb=" O ILE A 76 " pdb="NA NA A 803 " model vdw 2.213 2.470 nonbonded pdb=" OH TYR A 128 " pdb=" O LEU A 559 " model vdw 2.349 3.040 nonbonded pdb=" O TYR A 199 " pdb=" OG1 THR A 202 " model vdw 2.351 3.040 nonbonded pdb=" O MET A 407 " pdb=" OG1 THR A 411 " model vdw 2.375 3.040 ... (remaining 40903 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.015 0.077 4868 Z= 1.116 Angle : 2.211 10.580 6645 Z= 1.653 Chirality : 0.086 0.400 774 Planarity : 0.004 0.024 810 Dihedral : 13.820 67.617 1687 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 2.82 % Allowed : 5.24 % Favored : 91.94 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.29), residues: 605 helix: -1.18 (0.21), residues: 435 sheet: None (None), residues: 0 loop : -2.14 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A 300 TYR 0.028 0.004 TYR A 128 PHE 0.022 0.003 PHE A 534 TRP 0.020 0.003 TRP A 289 HIS 0.004 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.01516 / 1.11 ( 4863) covalent geometry : angle 2.20430 / 1.65 ( 6634) SS BOND : bond 0.05396 / 2.66 ( 4) SS BOND : angle 5.02663 / 2.89 ( 8) hydrogen bonds : bond 0.18337 / 12.47 ( 347) hydrogen bonds : angle 8.85252 / 6.49 ( 1041) link_NAG-ASN : bond 0.00660 / 0.35 ( 1) link_NAG-ASN : angle 3.85076 / 2.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.168 Fit side-chains REVERT: A 44 MET cc_start: 0.6684 (mtm) cc_final: 0.6401 (mpp) REVERT: A 49 ARG cc_start: 0.6199 (mtp-110) cc_final: 0.5792 (mtp-110) REVERT: A 62 MET cc_start: 0.8721 (mmp) cc_final: 0.8256 (mmm) REVERT: A 125 MET cc_start: 0.8536 (mmp) cc_final: 0.8292 (mmp) REVERT: A 136 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7011 (mtt-85) REVERT: A 168 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7482 (mm-40) REVERT: A 244 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 333 MET cc_start: 0.8938 (mtp) cc_final: 0.8358 (mtm) REVERT: A 342 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 382 MET cc_start: 0.7981 (mmm) cc_final: 0.7739 (mmm) REVERT: A 420 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6381 (ttp80) REVERT: A 445 GLN cc_start: 0.7284 (mm110) cc_final: 0.7061 (mm110) REVERT: A 483 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7163 (mm-40) REVERT: A 495 MET cc_start: 0.7536 (mtp) cc_final: 0.7104 (mtt) REVERT: A 513 GLN cc_start: 0.6490 (mm110) cc_final: 0.4947 (mp10) REVERT: A 548 THR cc_start: 0.7281 (m) cc_final: 0.6819 (p) REVERT: A 558 ARG cc_start: 0.6400 (ptt180) cc_final: 0.5862 (ptp90) REVERT: A 567 LYS cc_start: 0.2255 (OUTLIER) cc_final: 0.1624 (mttm) REVERT: A 651 ARG cc_start: 0.6584 (ttm110) cc_final: 0.5701 (tpp-160) outliers start: 14 outliers final: 1 residues processed: 92 average time/residue: 0.5769 time to fit residues: 55.0093 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 567 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 204 GLN A 295 GLN A 299 GLN A 399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.120070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.091907 restraints weight = 4921.039| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.48 r_work: 0.2761 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4868 Z= 0.158 Angle : 0.699 16.843 6645 Z= 0.346 Chirality : 0.044 0.159 774 Planarity : 0.005 0.039 810 Dihedral : 7.772 60.974 705 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.23 % Allowed : 7.86 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.33), residues: 605 helix: 1.08 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.63 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 267 TYR 0.016 0.002 TYR A 188 PHE 0.017 0.001 PHE A 453 TRP 0.017 0.001 TRP A 65 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 4863) covalent geometry : angle 0.69561 / 0.35 ( 6634) SS BOND : bond 0.00468 / 0.23 ( 4) SS BOND : angle 1.27083 / 0.85 ( 8) hydrogen bonds : bond 0.04753 / 3.25 ( 347) hydrogen bonds : angle 5.96404 / 4.41 ( 1041) link_NAG-ASN : bond 0.00075 / 0.04 ( 1) link_NAG-ASN : angle 2.90855 / 1.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.173 Fit side-chains REVERT: A 62 MET cc_start: 0.9255 (mmp) cc_final: 0.8910 (mmm) REVERT: A 167 GLN cc_start: 0.8304 (tt0) cc_final: 0.7874 (tt0) REVERT: A 168 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8344 (mm-40) REVERT: A 184 ILE cc_start: 0.8443 (mt) cc_final: 0.8190 (mm) REVERT: A 198 MET cc_start: 0.8944 (mtp) cc_final: 0.8699 (mtm) REVERT: A 206 PHE cc_start: 0.8249 (t80) cc_final: 0.7567 (t80) REVERT: A 300 ARG cc_start: 0.8500 (mmt-90) cc_final: 0.8196 (mpt180) REVERT: A 305 LYS cc_start: 0.8712 (tttp) cc_final: 0.8512 (tttt) REVERT: A 306 SER cc_start: 0.8437 (t) cc_final: 0.8204 (p) REVERT: A 333 MET cc_start: 0.9306 (mtp) cc_final: 0.8964 (mtm) REVERT: A 342 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: A 482 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 495 MET cc_start: 0.8224 (mtp) cc_final: 0.7864 (mtt) REVERT: A 513 GLN cc_start: 0.7061 (mm110) cc_final: 0.5420 (mp10) REVERT: A 651 ARG cc_start: 0.7242 (ttm110) cc_final: 0.6704 (ttm110) outliers start: 16 outliers final: 4 residues processed: 85 average time/residue: 0.4935 time to fit residues: 43.8552 Evaluate side-chains 62 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.119366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.091402 restraints weight = 4924.544| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.47 r_work: 0.2751 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4868 Z= 0.148 Angle : 0.643 13.597 6645 Z= 0.318 Chirality : 0.042 0.153 774 Planarity : 0.005 0.044 810 Dihedral : 7.196 58.954 701 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.83 % Allowed : 8.27 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.26 (0.34), residues: 605 helix: 1.52 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -1.27 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 300 TYR 0.015 0.002 TYR A 256 PHE 0.012 0.001 PHE A 453 TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 4863) covalent geometry : angle 0.64144 / 0.32 ( 6634) SS BOND : bond 0.00267 / 0.13 ( 4) SS BOND : angle 0.77323 / 0.40 ( 8) hydrogen bonds : bond 0.04413 / 3.04 ( 347) hydrogen bonds : angle 5.68071 / 4.21 ( 1041) link_NAG-ASN : bond 0.00148 / 0.08 ( 1) link_NAG-ASN : angle 1.86666 / 1.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.209 Fit side-chains REVERT: A 62 MET cc_start: 0.9254 (mmp) cc_final: 0.8924 (mmm) REVERT: A 167 GLN cc_start: 0.8384 (tt0) cc_final: 0.7951 (tt0) REVERT: A 168 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8333 (mm-40) REVERT: A 198 MET cc_start: 0.8961 (mtp) cc_final: 0.8706 (mtm) REVERT: A 206 PHE cc_start: 0.8303 (t80) cc_final: 0.7714 (t80) REVERT: A 300 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8150 (mpt180) REVERT: A 305 LYS cc_start: 0.8685 (tttp) cc_final: 0.8438 (tttt) REVERT: A 333 MET cc_start: 0.9301 (mtp) cc_final: 0.9015 (mtm) REVERT: A 495 MET cc_start: 0.8364 (mtp) cc_final: 0.7906 (mtt) REVERT: A 513 GLN cc_start: 0.6988 (mm110) cc_final: 0.5593 (mp10) REVERT: A 651 ARG cc_start: 0.7221 (ttm110) cc_final: 0.6748 (ttm110) outliers start: 19 outliers final: 5 residues processed: 66 average time/residue: 0.4702 time to fit residues: 32.4826 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.093620 restraints weight = 4958.598| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.49 r_work: 0.2783 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4868 Z= 0.126 Angle : 0.600 11.282 6645 Z= 0.297 Chirality : 0.041 0.149 774 Planarity : 0.005 0.048 810 Dihedral : 6.093 58.052 697 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.02 % Allowed : 10.48 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.34), residues: 605 helix: 1.76 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -1.06 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 267 TYR 0.015 0.001 TYR A 256 PHE 0.009 0.001 PHE A 453 TRP 0.011 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 4863) covalent geometry : angle 0.59877 / 0.30 ( 6634) SS BOND : bond 0.00174 / 0.08 ( 4) SS BOND : angle 0.56551 / 0.26 ( 8) hydrogen bonds : bond 0.04015 / 2.77 ( 347) hydrogen bonds : angle 5.49265 / 4.07 ( 1041) link_NAG-ASN : bond 0.00184 / 0.10 ( 1) link_NAG-ASN : angle 1.78373 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.176 Fit side-chains REVERT: A 62 MET cc_start: 0.9247 (mmp) cc_final: 0.8952 (mmm) REVERT: A 103 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7987 (mt) REVERT: A 167 GLN cc_start: 0.8308 (tt0) cc_final: 0.7805 (tt0) REVERT: A 198 MET cc_start: 0.8831 (mtp) cc_final: 0.8541 (mtm) REVERT: A 206 PHE cc_start: 0.8341 (t80) cc_final: 0.7700 (t80) REVERT: A 300 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8145 (mpt180) REVERT: A 333 MET cc_start: 0.9253 (mtp) cc_final: 0.8954 (mtm) REVERT: A 342 GLU cc_start: 0.8427 (mp0) cc_final: 0.7940 (mp0) REVERT: A 482 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 495 MET cc_start: 0.8270 (mtp) cc_final: 0.7797 (mtt) REVERT: A 513 GLN cc_start: 0.6989 (mm110) cc_final: 0.5633 (mp10) REVERT: A 557 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6107 (m-70) REVERT: A 651 ARG cc_start: 0.7098 (ttm110) cc_final: 0.6665 (ttm110) REVERT: B 31 MET cc_start: 0.7198 (mmt) cc_final: 0.6171 (ptp) outliers start: 15 outliers final: 6 residues processed: 72 average time/residue: 0.5339 time to fit residues: 40.1295 Evaluate side-chains 61 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.094115 restraints weight = 4967.100| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.49 r_work: 0.2788 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4868 Z= 0.126 Angle : 0.604 10.220 6645 Z= 0.298 Chirality : 0.041 0.148 774 Planarity : 0.005 0.050 810 Dihedral : 5.215 37.094 694 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.23 % Allowed : 11.49 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.35), residues: 605 helix: 1.85 (0.24), residues: 455 sheet: None (None), residues: 0 loop : -0.92 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 558 TYR 0.012 0.001 TYR A 256 PHE 0.009 0.001 PHE A 534 TRP 0.010 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 4863) covalent geometry : angle 0.60219 / 0.30 ( 6634) SS BOND : bond 0.00382 / 0.18 ( 4) SS BOND : angle 1.30933 / 1.05 ( 8) hydrogen bonds : bond 0.03989 / 2.76 ( 347) hydrogen bonds : angle 5.44154 / 4.04 ( 1041) link_NAG-ASN : bond 0.00180 / 0.09 ( 1) link_NAG-ASN : angle 1.69702 / 1.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.197 Fit side-chains REVERT: A 62 MET cc_start: 0.9262 (mmp) cc_final: 0.8923 (mmm) REVERT: A 103 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8020 (mt) REVERT: A 125 MET cc_start: 0.8832 (mmp) cc_final: 0.8395 (mmp) REVERT: A 167 GLN cc_start: 0.8239 (tt0) cc_final: 0.7837 (tt0) REVERT: A 198 MET cc_start: 0.8870 (mtp) cc_final: 0.8591 (mtm) REVERT: A 206 PHE cc_start: 0.8390 (t80) cc_final: 0.7791 (t80) REVERT: A 241 THR cc_start: 0.9049 (p) cc_final: 0.8813 (p) REVERT: A 300 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8179 (mpt180) REVERT: A 333 MET cc_start: 0.9262 (mtp) cc_final: 0.8976 (mtm) REVERT: A 342 GLU cc_start: 0.8502 (mp0) cc_final: 0.8260 (mp0) REVERT: A 482 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 495 MET cc_start: 0.8335 (mtp) cc_final: 0.7881 (mtt) REVERT: A 513 GLN cc_start: 0.7114 (mm110) cc_final: 0.5739 (mp10) REVERT: A 557 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.6133 (m-70) REVERT: A 651 ARG cc_start: 0.7157 (ttm110) cc_final: 0.6730 (ttm110) REVERT: B 31 MET cc_start: 0.7198 (mmt) cc_final: 0.6208 (ptp) outliers start: 16 outliers final: 5 residues processed: 72 average time/residue: 0.4965 time to fit residues: 37.3708 Evaluate side-chains 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.093480 restraints weight = 4983.823| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.49 r_work: 0.2780 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4868 Z= 0.132 Angle : 0.603 9.423 6645 Z= 0.297 Chirality : 0.041 0.150 774 Planarity : 0.005 0.050 810 Dihedral : 5.152 36.965 694 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.42 % Allowed : 12.70 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.86 (0.35), residues: 605 helix: 1.88 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.75 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.012 0.001 TYR A 128 PHE 0.010 0.001 PHE A 534 TRP 0.009 0.001 TRP A 65 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 4863) covalent geometry : angle 0.60108 / 0.30 ( 6634) SS BOND : bond 0.00316 / 0.15 ( 4) SS BOND : angle 1.05905 / 0.68 ( 8) hydrogen bonds : bond 0.04107 / 2.86 ( 347) hydrogen bonds : angle 5.44941 / 4.04 ( 1041) link_NAG-ASN : bond 0.00170 / 0.09 ( 1) link_NAG-ASN : angle 1.64432 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.174 Fit side-chains REVERT: A 62 MET cc_start: 0.9275 (mmp) cc_final: 0.8941 (mmm) REVERT: A 103 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 198 MET cc_start: 0.8892 (mtp) cc_final: 0.8613 (mtm) REVERT: A 206 PHE cc_start: 0.8420 (t80) cc_final: 0.7824 (t80) REVERT: A 241 THR cc_start: 0.9027 (p) cc_final: 0.8790 (p) REVERT: A 300 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8163 (mpt180) REVERT: A 333 MET cc_start: 0.9273 (mtp) cc_final: 0.8994 (mtm) REVERT: A 342 GLU cc_start: 0.8526 (mp0) cc_final: 0.8241 (mp0) REVERT: A 482 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 495 MET cc_start: 0.8338 (mtp) cc_final: 0.7854 (mtt) REVERT: A 513 GLN cc_start: 0.6999 (mm110) cc_final: 0.5579 (mt0) REVERT: A 557 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.6025 (m-70) REVERT: A 651 ARG cc_start: 0.7156 (ttm110) cc_final: 0.6755 (ttm110) REVERT: B 31 MET cc_start: 0.7226 (mmt) cc_final: 0.6246 (ptp) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.5054 time to fit residues: 34.3399 Evaluate side-chains 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.090982 restraints weight = 4963.560| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.49 r_work: 0.2746 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4868 Z= 0.155 Angle : 0.631 9.509 6645 Z= 0.311 Chirality : 0.043 0.155 774 Planarity : 0.005 0.050 810 Dihedral : 5.270 37.201 694 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.02 % Allowed : 13.91 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.34), residues: 605 helix: 1.81 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.72 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.015 0.002 TYR A 128 PHE 0.012 0.001 PHE A 534 TRP 0.009 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 4863) covalent geometry : angle 0.62987 / 0.31 ( 6634) SS BOND : bond 0.00350 / 0.17 ( 4) SS BOND : angle 0.99314 / 0.58 ( 8) hydrogen bonds : bond 0.04404 / 3.05 ( 347) hydrogen bonds : angle 5.55454 / 4.12 ( 1041) link_NAG-ASN : bond 0.00144 / 0.08 ( 1) link_NAG-ASN : angle 1.64629 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.108 Fit side-chains REVERT: A 62 MET cc_start: 0.9239 (mmp) cc_final: 0.8930 (mmm) REVERT: A 103 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8117 (mt) REVERT: A 206 PHE cc_start: 0.8410 (t80) cc_final: 0.7752 (t80) REVERT: A 241 THR cc_start: 0.9147 (p) cc_final: 0.8894 (p) REVERT: A 300 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8231 (mpt180) REVERT: A 333 MET cc_start: 0.9254 (mtp) cc_final: 0.8940 (mtm) REVERT: A 342 GLU cc_start: 0.8548 (mp0) cc_final: 0.8280 (mp0) REVERT: A 482 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8293 (tm-30) REVERT: A 495 MET cc_start: 0.8350 (mtp) cc_final: 0.7839 (mtt) REVERT: A 513 GLN cc_start: 0.6914 (mm110) cc_final: 0.5440 (mp10) REVERT: A 557 HIS cc_start: 0.6703 (OUTLIER) cc_final: 0.6119 (m-70) REVERT: A 651 ARG cc_start: 0.7227 (ttm110) cc_final: 0.6769 (ttm110) REVERT: B 31 MET cc_start: 0.7235 (mmt) cc_final: 0.6159 (mtp) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.5031 time to fit residues: 33.6887 Evaluate side-chains 64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.120512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.092233 restraints weight = 4997.606| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.52 r_work: 0.2764 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4868 Z= 0.138 Angle : 0.627 9.331 6645 Z= 0.306 Chirality : 0.042 0.157 774 Planarity : 0.005 0.050 810 Dihedral : 5.199 36.813 694 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.22 % Allowed : 14.11 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.34), residues: 605 helix: 1.87 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.59 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.012 0.001 TYR A 128 PHE 0.010 0.001 PHE A 534 TRP 0.009 0.001 TRP A 65 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4863) covalent geometry : angle 0.62586 / 0.31 ( 6634) SS BOND : bond 0.00278 / 0.14 ( 4) SS BOND : angle 0.84038 / 0.43 ( 8) hydrogen bonds : bond 0.04187 / 2.90 ( 347) hydrogen bonds : angle 5.49129 / 4.08 ( 1041) link_NAG-ASN : bond 0.01600 / 0.84 ( 1) link_NAG-ASN : angle 1.69948 / 1.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.173 Fit side-chains REVERT: A 62 MET cc_start: 0.9250 (mmp) cc_final: 0.8916 (mmm) REVERT: A 103 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8095 (mt) REVERT: A 198 MET cc_start: 0.8855 (mtp) cc_final: 0.8576 (mtm) REVERT: A 206 PHE cc_start: 0.8370 (t80) cc_final: 0.7744 (t80) REVERT: A 241 THR cc_start: 0.9016 (p) cc_final: 0.8772 (p) REVERT: A 300 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8127 (mpt180) REVERT: A 333 MET cc_start: 0.9243 (mtp) cc_final: 0.8917 (mtm) REVERT: A 342 GLU cc_start: 0.8541 (mp0) cc_final: 0.8285 (mp0) REVERT: A 482 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8275 (tm-30) REVERT: A 495 MET cc_start: 0.8325 (mtp) cc_final: 0.7817 (mtt) REVERT: A 513 GLN cc_start: 0.6913 (mm110) cc_final: 0.5465 (mp10) REVERT: A 557 HIS cc_start: 0.6609 (OUTLIER) cc_final: 0.6041 (m-70) REVERT: A 651 ARG cc_start: 0.7199 (ttm110) cc_final: 0.6738 (ttm110) REVERT: B 31 MET cc_start: 0.7167 (mmt) cc_final: 0.6163 (ptp) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 0.4568 time to fit residues: 31.0143 Evaluate side-chains 66 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.122892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.094785 restraints weight = 4957.158| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.52 r_work: 0.2796 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4868 Z= 0.123 Angle : 0.603 9.209 6645 Z= 0.293 Chirality : 0.041 0.150 774 Planarity : 0.005 0.050 810 Dihedral : 5.027 36.376 694 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.02 % Allowed : 13.91 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.07 (0.35), residues: 605 helix: 2.01 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -0.55 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.012 0.001 TYR A 256 PHE 0.010 0.001 PHE A 534 TRP 0.011 0.001 TRP A 65 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 4863) covalent geometry : angle 0.60122 / 0.29 ( 6634) SS BOND : bond 0.00215 / 0.10 ( 4) SS BOND : angle 0.77279 / 0.41 ( 8) hydrogen bonds : bond 0.03951 / 2.74 ( 347) hydrogen bonds : angle 5.38681 / 4.00 ( 1041) link_NAG-ASN : bond 0.01052 / 0.55 ( 1) link_NAG-ASN : angle 1.78480 / 1.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.191 Fit side-chains REVERT: A 62 MET cc_start: 0.9252 (mmp) cc_final: 0.8935 (mmm) REVERT: A 206 PHE cc_start: 0.8357 (t80) cc_final: 0.7780 (t80) REVERT: A 300 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8140 (mpt180) REVERT: A 333 MET cc_start: 0.9247 (mtp) cc_final: 0.9005 (mtm) REVERT: A 342 GLU cc_start: 0.8549 (mp0) cc_final: 0.8293 (mp0) REVERT: A 482 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 495 MET cc_start: 0.8296 (mtp) cc_final: 0.7835 (mtt) REVERT: A 513 GLN cc_start: 0.6854 (mm110) cc_final: 0.5489 (mt0) REVERT: A 557 HIS cc_start: 0.6486 (OUTLIER) cc_final: 0.5940 (m-70) REVERT: A 651 ARG cc_start: 0.7159 (ttm110) cc_final: 0.6708 (ttm110) REVERT: B 31 MET cc_start: 0.7194 (mmt) cc_final: 0.6150 (mtp) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.4718 time to fit residues: 30.5573 Evaluate side-chains 64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.092264 restraints weight = 4904.328| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.47 r_work: 0.2737 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4868 Z= 0.166 Angle : 0.651 10.101 6645 Z= 0.319 Chirality : 0.044 0.158 774 Planarity : 0.005 0.050 810 Dihedral : 5.284 37.283 694 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.61 % Allowed : 14.52 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.34), residues: 605 helix: 1.77 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -0.54 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.016 0.002 TYR A 128 PHE 0.013 0.002 PHE A 534 TRP 0.010 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 4863) covalent geometry : angle 0.64931 / 0.32 ( 6634) SS BOND : bond 0.00332 / 0.16 ( 4) SS BOND : angle 0.93573 / 0.49 ( 8) hydrogen bonds : bond 0.04543 / 3.15 ( 347) hydrogen bonds : angle 5.60975 / 4.17 ( 1041) link_NAG-ASN : bond 0.00976 / 0.51 ( 1) link_NAG-ASN : angle 1.95815 / 1.78 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.110 Fit side-chains REVERT: A 62 MET cc_start: 0.9254 (mmp) cc_final: 0.8961 (mmm) REVERT: A 206 PHE cc_start: 0.8439 (t80) cc_final: 0.7791 (t80) REVERT: A 300 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8220 (mpt180) REVERT: A 306 SER cc_start: 0.8479 (t) cc_final: 0.8262 (p) REVERT: A 333 MET cc_start: 0.9263 (mtp) cc_final: 0.8967 (mtm) REVERT: A 342 GLU cc_start: 0.8550 (mp0) cc_final: 0.8316 (mp0) REVERT: A 482 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 495 MET cc_start: 0.8278 (mtp) cc_final: 0.7868 (mtt) REVERT: A 513 GLN cc_start: 0.6898 (mm110) cc_final: 0.5507 (mt0) REVERT: A 557 HIS cc_start: 0.6771 (OUTLIER) cc_final: 0.6187 (m-70) REVERT: A 651 ARG cc_start: 0.7278 (ttm110) cc_final: 0.6792 (ttm110) REVERT: B 31 MET cc_start: 0.7238 (mmt) cc_final: 0.6180 (mtp) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.4385 time to fit residues: 28.8037 Evaluate side-chains 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.124143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.096618 restraints weight = 4996.485| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.46 r_work: 0.2820 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4868 Z= 0.116 Angle : 0.595 9.601 6645 Z= 0.289 Chirality : 0.040 0.149 774 Planarity : 0.005 0.050 810 Dihedral : 4.947 35.983 694 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.01 % Allowed : 14.92 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.35), residues: 605 helix: 2.06 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.39 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.012 0.001 TYR A 256 PHE 0.009 0.001 PHE A 534 TRP 0.013 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 4863) covalent geometry : angle 0.59347 / 0.29 ( 6634) SS BOND : bond 0.00222 / 0.11 ( 4) SS BOND : angle 0.68845 / 0.34 ( 8) hydrogen bonds : bond 0.03813 / 2.66 ( 347) hydrogen bonds : angle 5.35550 / 3.98 ( 1041) link_NAG-ASN : bond 0.00780 / 0.41 ( 1) link_NAG-ASN : angle 1.72896 / 1.43 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1538.80 seconds wall clock time: 27 minutes 2.96 seconds (1622.96 seconds total)