Starting phenix.real_space_refine on Fri Aug 22 15:07:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hez_34705/08_2025/8hez_34705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hez_34705/08_2025/8hez_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_34705/08_2025/8hez_34705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hez_34705/08_2025/8hez_34705.map" model { file = "/net/cci-nas-00/data/ceres_data/8hez_34705/08_2025/8hez_34705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hez_34705/08_2025/8hez_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-2.0-5787/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.71, per 1000 atoms: 0.36 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: 0.52 Conformation dependent library (CDL) restraints added in 214.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.11 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: 0.72 Time building geometry restraints manager: 0.67 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: 2450 13.53 - 27.05: 262 27.05 - 40.57: 86 40.57 - 54.09: 21 54.09 - 67.62: 9 Dihedral angle restraints: 2828 sinusoidal: 1088 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 2825 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: 0.140 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 13.748 67.617 1708 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 aren 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 covalent geometry : bond 0.01516 ( 4863) covalent geometry : angle 2.20430 ( 6634) SS BOND : bond 0.05396 ( 4) SS BOND : angle 5.02663 ( 8) hydrogen bonds : bond 0.18337 ( 347) hydrogen bonds : angle 8.85252 ( 1041) link_NAG-ASN : bond 0.00660 ( 1) link_NAG-ASN : angle 3.85076 ( 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 : 0.196 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: 0.6731 time to fit residues: 64.0084 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 : 0.171 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3258 r_free = 0.3258 target = 0.120198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.092581 restraints weight = 4917.415| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.41 r_work: 0.2772 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4868 Z= 0.159 Angle : 0.696 16.790 6645 Z= 0.345 Chirality : 0.043 0.154 774 Planarity : 0.005 0.039 810 Dihedral : 7.653 61.332 726 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 : 3.43 % Allowed : 7.86 % Favored : 88.71 % 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 aren not related in a simple way. whole: 0.57 (0.33), residues: 605 helix: 1.07 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.62 (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 covalent geometry : bond 0.00349 ( 4863) covalent geometry : angle 0.69278 ( 6634) SS BOND : bond 0.00488 ( 4) SS BOND : angle 1.26792 ( 8) hydrogen bonds : bond 0.04787 ( 347) hydrogen bonds : angle 5.97025 ( 1041) link_NAG-ASN : bond 0.00048 ( 1) link_NAG-ASN : angle 2.83561 ( 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 86 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.207 Fit side-chains REVERT: A 62 MET cc_start: 0.9272 (mmp) cc_final: 0.8929 (mmm) REVERT: A 167 GLN cc_start: 0.8319 (tt0) cc_final: 0.7906 (tt0) REVERT: A 184 ILE cc_start: 0.8548 (mt) cc_final: 0.8315 (mm) REVERT: A 198 MET cc_start: 0.8978 (mtp) cc_final: 0.8736 (mtm) REVERT: A 206 PHE cc_start: 0.8279 (t80) cc_final: 0.7636 (t80) REVERT: A 300 ARG cc_start: 0.8495 (mmt-90) cc_final: 0.8194 (mpt180) REVERT: A 333 MET cc_start: 0.9326 (mtp) cc_final: 0.8994 (mtm) REVERT: A 342 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: A 482 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 495 MET cc_start: 0.8264 (mtp) cc_final: 0.7923 (mtt) REVERT: A 513 GLN cc_start: 0.7106 (mm110) cc_final: 0.5505 (mp10) REVERT: A 651 ARG cc_start: 0.7276 (ttm110) cc_final: 0.6785 (ttm110) outliers start: 17 outliers final: 4 residues processed: 80 average time/residue: 0.5465 time to fit residues: 45.6466 Evaluate side-chains 61 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.118307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.090306 restraints weight = 4934.794| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.48 r_work: 0.2750 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4868 Z= 0.159 Angle : 0.655 14.282 6645 Z= 0.325 Chirality : 0.043 0.156 774 Planarity : 0.005 0.046 810 Dihedral : 6.469 57.065 719 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.23 % Allowed : 9.27 % Favored : 87.50 % 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 aren not related in a simple way. whole: 1.17 (0.34), residues: 605 helix: 1.46 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -1.26 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 300 TYR 0.015 0.002 TYR A 256 PHE 0.013 0.002 PHE A 453 TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4863) covalent geometry : angle 0.65370 ( 6634) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.80590 ( 8) hydrogen bonds : bond 0.04583 ( 347) hydrogen bonds : angle 5.75813 ( 1041) link_NAG-ASN : bond 0.00120 ( 1) link_NAG-ASN : angle 2.13255 ( 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 71 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.187 Fit side-chains REVERT: A 62 MET cc_start: 0.9269 (mmp) cc_final: 0.8946 (mmm) REVERT: A 167 GLN cc_start: 0.8375 (tt0) cc_final: 0.7911 (tt0) REVERT: A 198 MET cc_start: 0.8995 (mtp) cc_final: 0.8731 (mtm) REVERT: A 206 PHE cc_start: 0.8350 (t80) cc_final: 0.7740 (t80) REVERT: A 300 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8144 (mpt180) REVERT: A 333 MET cc_start: 0.9313 (mtp) cc_final: 0.9030 (mtm) REVERT: A 495 MET cc_start: 0.8299 (mtp) cc_final: 0.7925 (mtt) REVERT: A 513 GLN cc_start: 0.7013 (mm110) cc_final: 0.5595 (mp10) REVERT: A 651 ARG cc_start: 0.7254 (ttm110) cc_final: 0.6795 (ttm170) outliers start: 16 outliers final: 4 residues processed: 64 average time/residue: 0.5159 time to fit residues: 34.6277 Evaluate side-chains 60 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.120292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.092429 restraints weight = 4971.727| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.48 r_work: 0.2764 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4868 Z= 0.136 Angle : 0.613 11.929 6645 Z= 0.304 Chirality : 0.041 0.152 774 Planarity : 0.005 0.050 810 Dihedral : 5.313 37.472 715 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.02 % Allowed : 11.29 % Favored : 85.69 % 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 aren not related in a simple way. whole: 1.52 (0.34), residues: 605 helix: 1.69 (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 0.002 0.000 ARG A 267 TYR 0.013 0.002 TYR A 256 PHE 0.010 0.001 PHE A 453 TRP 0.012 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4863) covalent geometry : angle 0.61193 ( 6634) SS BOND : bond 0.00349 ( 4) SS BOND : angle 0.60438 ( 8) hydrogen bonds : bond 0.04187 ( 347) hydrogen bonds : angle 5.58152 ( 1041) link_NAG-ASN : bond 0.00171 ( 1) link_NAG-ASN : angle 1.96209 ( 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 : 0.181 Fit side-chains REVERT: A 62 MET cc_start: 0.9252 (mmp) cc_final: 0.8877 (mmm) REVERT: A 103 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8031 (mt) REVERT: A 167 GLN cc_start: 0.8355 (tt0) cc_final: 0.7882 (tt0) REVERT: A 198 MET cc_start: 0.8927 (mtp) cc_final: 0.8641 (mtm) REVERT: A 206 PHE cc_start: 0.8402 (t80) cc_final: 0.7738 (t80) REVERT: A 300 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8162 (mpt180) REVERT: A 333 MET cc_start: 0.9274 (mtp) cc_final: 0.8991 (mtm) REVERT: A 342 GLU cc_start: 0.8515 (mp0) cc_final: 0.8082 (mp0) REVERT: A 482 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 495 MET cc_start: 0.8326 (mtp) cc_final: 0.7854 (mtt) REVERT: A 513 GLN cc_start: 0.7013 (mm110) cc_final: 0.5608 (mp10) REVERT: A 651 ARG cc_start: 0.7159 (ttm110) cc_final: 0.6731 (ttm110) REVERT: B 31 MET cc_start: 0.7314 (mmt) cc_final: 0.6270 (ptp) outliers start: 15 outliers final: 6 residues processed: 72 average time/residue: 0.5713 time to fit residues: 42.8578 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 391 MET Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.117700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.089675 restraints weight = 5011.158| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.49 r_work: 0.2730 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4868 Z= 0.167 Angle : 0.649 11.048 6645 Z= 0.322 Chirality : 0.043 0.157 774 Planarity : 0.005 0.051 810 Dihedral : 5.379 37.841 715 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.42 % Allowed : 12.50 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.34), residues: 605 helix: 1.60 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.016 0.002 TYR A 128 PHE 0.012 0.002 PHE A 534 TRP 0.009 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4863) covalent geometry : angle 0.64626 ( 6634) SS BOND : bond 0.00530 ( 4) SS BOND : angle 1.48672 ( 8) hydrogen bonds : bond 0.04527 ( 347) hydrogen bonds : angle 5.66737 ( 1041) link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 1.96341 ( 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 71 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.186 Fit side-chains REVERT: A 62 MET cc_start: 0.9248 (mmp) cc_final: 0.8975 (mmm) REVERT: A 103 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 167 GLN cc_start: 0.8232 (tt0) cc_final: 0.7810 (tt0) REVERT: A 206 PHE cc_start: 0.8394 (t80) cc_final: 0.7697 (t80) REVERT: A 241 THR cc_start: 0.9053 (p) cc_final: 0.8835 (p) REVERT: A 300 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8237 (mpt180) REVERT: A 333 MET cc_start: 0.9252 (mtp) cc_final: 0.8972 (mtm) REVERT: A 342 GLU cc_start: 0.8560 (mp0) cc_final: 0.8294 (mp0) REVERT: A 482 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 495 MET cc_start: 0.8352 (mtp) cc_final: 0.7822 (mtt) REVERT: A 513 GLN cc_start: 0.7050 (mm110) cc_final: 0.5629 (mp10) REVERT: A 651 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6738 (ttm110) outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.5517 time to fit residues: 38.6137 Evaluate side-chains 61 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 391 MET Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.122355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.094521 restraints weight = 5010.903| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.51 r_work: 0.2799 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4868 Z= 0.118 Angle : 0.593 10.034 6645 Z= 0.291 Chirality : 0.040 0.146 774 Planarity : 0.005 0.051 810 Dihedral : 5.032 36.658 715 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 13.31 % Favored : 84.68 % 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 aren not related in a simple way. whole: 1.84 (0.34), residues: 605 helix: 1.86 (0.24), residues: 455 sheet: None (None), residues: 0 loop : -0.75 (0.52), 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 0.012 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4863) covalent geometry : angle 0.59175 ( 6634) SS BOND : bond 0.00252 ( 4) SS BOND : angle 0.97038 ( 8) hydrogen bonds : bond 0.03856 ( 347) hydrogen bonds : angle 5.40325 ( 1041) link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 1.71827 ( 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 68 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.190 Fit side-chains REVERT: A 62 MET cc_start: 0.9258 (mmp) cc_final: 0.8958 (mmm) REVERT: A 103 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8071 (mt) REVERT: A 206 PHE cc_start: 0.8362 (t80) cc_final: 0.7768 (t80) REVERT: A 241 THR cc_start: 0.9032 (p) cc_final: 0.8797 (p) REVERT: A 300 ARG cc_start: 0.8527 (mmt-90) cc_final: 0.8151 (mpt180) REVERT: A 333 MET cc_start: 0.9253 (mtp) cc_final: 0.8969 (mtm) REVERT: A 342 GLU cc_start: 0.8535 (mp0) cc_final: 0.8243 (mp0) REVERT: A 482 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8095 (tm-30) REVERT: A 495 MET cc_start: 0.8314 (mtp) cc_final: 0.7849 (mtt) REVERT: A 513 GLN cc_start: 0.6934 (mm110) cc_final: 0.5462 (mp10) REVERT: A 557 HIS cc_start: 0.6578 (m-70) cc_final: 0.6038 (m-70) REVERT: A 651 ARG cc_start: 0.7168 (ttm110) cc_final: 0.6741 (ttm110) REVERT: B 31 MET cc_start: 0.7244 (mmt) cc_final: 0.6206 (ptp) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 0.5523 time to fit residues: 37.5004 Evaluate side-chains 60 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 539 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 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 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098164 restraints weight = 4877.697| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.49 r_work: 0.2816 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4868 Z= 0.116 Angle : 0.588 9.273 6645 Z= 0.287 Chirality : 0.040 0.146 774 Planarity : 0.005 0.052 810 Dihedral : 4.910 36.665 715 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.62 % Allowed : 13.10 % Favored : 84.27 % 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 aren not related in a simple way. whole: 2.05 (0.35), residues: 605 helix: 2.01 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -0.68 (0.52), residues: 149 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 0.014 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4863) covalent geometry : angle 0.58684 ( 6634) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.79866 ( 8) hydrogen bonds : bond 0.03781 ( 347) hydrogen bonds : angle 5.31630 ( 1041) link_NAG-ASN : bond 0.00199 ( 1) link_NAG-ASN : angle 1.53947 ( 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 73 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.194 Fit side-chains REVERT: A 62 MET cc_start: 0.9278 (mmp) cc_final: 0.8937 (mmm) REVERT: A 206 PHE cc_start: 0.8328 (t80) cc_final: 0.7806 (t80) REVERT: A 241 THR cc_start: 0.9030 (p) cc_final: 0.8790 (p) REVERT: A 300 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8104 (mpt180) REVERT: A 333 MET cc_start: 0.9261 (mtp) cc_final: 0.9025 (mtm) REVERT: A 342 GLU cc_start: 0.8540 (mp0) cc_final: 0.8257 (mp0) REVERT: A 482 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 495 MET cc_start: 0.8234 (mtp) cc_final: 0.7788 (mtt) REVERT: A 513 GLN cc_start: 0.6966 (mm110) cc_final: 0.5546 (mt0) REVERT: A 557 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.6009 (m-70) REVERT: A 651 ARG cc_start: 0.7194 (ttm110) cc_final: 0.6768 (ttm110) REVERT: B 31 MET cc_start: 0.7205 (mmt) cc_final: 0.6212 (ptp) outliers start: 13 outliers final: 5 residues processed: 67 average time/residue: 0.5362 time to fit residues: 37.5735 Evaluate side-chains 62 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.126420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.098623 restraints weight = 4951.711| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.50 r_work: 0.2817 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4868 Z= 0.115 Angle : 0.583 8.845 6645 Z= 0.285 Chirality : 0.040 0.147 774 Planarity : 0.005 0.051 810 Dihedral : 4.844 36.402 715 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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 aren not related in a simple way. whole: 2.17 (0.35), residues: 605 helix: 2.10 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 151 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 0.011 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4863) covalent geometry : angle 0.58244 ( 6634) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.71172 ( 8) hydrogen bonds : bond 0.03769 ( 347) hydrogen bonds : angle 5.29910 ( 1041) link_NAG-ASN : bond 0.00195 ( 1) link_NAG-ASN : angle 1.50353 ( 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 67 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.191 Fit side-chains REVERT: A 44 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7163 (mpp) REVERT: A 62 MET cc_start: 0.9275 (mmp) cc_final: 0.8976 (mmm) REVERT: A 206 PHE cc_start: 0.8351 (t80) cc_final: 0.7840 (t80) REVERT: A 241 THR cc_start: 0.9031 (p) cc_final: 0.8782 (p) REVERT: A 300 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8182 (mpt180) REVERT: A 333 MET cc_start: 0.9259 (mtp) cc_final: 0.9024 (mtm) REVERT: A 342 GLU cc_start: 0.8516 (mp0) cc_final: 0.8249 (mp0) REVERT: A 482 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8098 (tm-30) REVERT: A 495 MET cc_start: 0.8228 (mtp) cc_final: 0.7777 (mtt) REVERT: A 513 GLN cc_start: 0.6860 (mm110) cc_final: 0.5513 (mt0) REVERT: A 557 HIS cc_start: 0.6307 (OUTLIER) cc_final: 0.5805 (m-70) REVERT: A 651 ARG cc_start: 0.7225 (ttm110) cc_final: 0.6752 (ttm110) REVERT: B 31 MET cc_start: 0.7384 (mmt) cc_final: 0.6348 (ptp) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.5722 time to fit residues: 36.3926 Evaluate side-chains 62 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 MET 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 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: 5.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 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 = 0.3247 r_free = 0.3247 target = 0.119648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.091432 restraints weight = 4996.601| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.50 r_work: 0.2752 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4868 Z= 0.151 Angle : 0.628 9.221 6645 Z= 0.309 Chirality : 0.042 0.156 774 Planarity : 0.005 0.051 810 Dihedral : 5.091 37.257 715 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.22 % Allowed : 14.31 % Favored : 83.47 % 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 aren not related in a simple way. whole: 1.96 (0.34), residues: 605 helix: 1.93 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.62 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.015 0.002 TYR A 128 PHE 0.012 0.001 PHE A 534 TRP 0.010 0.001 TRP A 429 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4863) covalent geometry : angle 0.62695 ( 6634) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.90593 ( 8) hydrogen bonds : bond 0.04356 ( 347) hydrogen bonds : angle 5.51719 ( 1041) link_NAG-ASN : bond 0.00150 ( 1) link_NAG-ASN : angle 1.52212 ( 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 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.177 Fit side-chains REVERT: A 44 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6973 (mpp) REVERT: A 62 MET cc_start: 0.9254 (mmp) cc_final: 0.8884 (mmm) REVERT: A 206 PHE cc_start: 0.8389 (t80) cc_final: 0.7749 (t80) REVERT: A 241 THR cc_start: 0.9131 (p) cc_final: 0.8886 (p) REVERT: A 300 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8132 (mpt180) REVERT: A 333 MET cc_start: 0.9248 (mtp) cc_final: 0.8932 (mtm) REVERT: A 342 GLU cc_start: 0.8543 (mp0) cc_final: 0.8296 (mp0) REVERT: A 482 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8378 (tm-30) REVERT: A 495 MET cc_start: 0.8311 (mtp) cc_final: 0.7800 (mtt) REVERT: A 557 HIS cc_start: 0.6519 (OUTLIER) cc_final: 0.5964 (m-70) REVERT: A 651 ARG cc_start: 0.7194 (ttm110) cc_final: 0.6731 (ttm110) REVERT: B 31 MET cc_start: 0.7166 (mmt) cc_final: 0.6120 (mtp) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.5547 time to fit residues: 34.7574 Evaluate side-chains 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 129 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 38 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.122161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.093933 restraints weight = 4915.485| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.51 r_work: 0.2782 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3043 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= 0.128 Angle : 0.613 9.168 6645 Z= 0.299 Chirality : 0.041 0.148 774 Planarity : 0.005 0.050 810 Dihedral : 5.196 36.582 715 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.22 % Allowed : 14.92 % Favored : 82.86 % 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 aren not related in a simple way. whole: 2.08 (0.34), residues: 605 helix: 2.02 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.56 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.011 0.001 TYR A 128 PHE 0.011 0.001 PHE A 148 TRP 0.011 0.001 TRP A 65 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4863) covalent geometry : angle 0.61145 ( 6634) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.78073 ( 8) hydrogen bonds : bond 0.04044 ( 347) hydrogen bonds : angle 5.41449 ( 1041) link_NAG-ASN : bond 0.01883 ( 1) link_NAG-ASN : angle 1.70936 ( 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 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.188 Fit side-chains REVERT: A 44 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7165 (mpp) REVERT: A 62 MET cc_start: 0.9259 (mmp) cc_final: 0.8959 (mmm) REVERT: A 206 PHE cc_start: 0.8359 (t80) cc_final: 0.7783 (t80) REVERT: A 300 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8134 (mpt180) REVERT: A 333 MET cc_start: 0.9240 (mtp) cc_final: 0.8963 (mtm) REVERT: A 342 GLU cc_start: 0.8528 (mp0) cc_final: 0.8290 (mp0) REVERT: A 482 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 495 MET cc_start: 0.8291 (mtp) cc_final: 0.7800 (mtt) REVERT: A 557 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.5950 (m-70) REVERT: A 651 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6705 (ttm110) REVERT: B 31 MET cc_start: 0.7168 (mmt) cc_final: 0.6166 (ptp) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.5784 time to fit residues: 36.1925 Evaluate side-chains 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 391 MET 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: 0.8980 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.126094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.098717 restraints weight = 5001.210| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.48 r_work: 0.2852 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4868 Z= 0.112 Angle : 0.583 10.044 6645 Z= 0.283 Chirality : 0.040 0.174 774 Planarity : 0.005 0.050 810 Dihedral : 4.860 36.029 715 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.22 % Allowed : 14.72 % Favored : 83.06 % 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 aren not related in a simple way. whole: 2.32 (0.35), residues: 605 helix: 2.19 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -0.49 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 558 TYR 0.011 0.001 TYR A 256 PHE 0.008 0.001 PHE A 534 TRP 0.014 0.001 TRP A 65 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 4863) covalent geometry : angle 0.58131 ( 6634) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.65094 ( 8) hydrogen bonds : bond 0.03672 ( 347) hydrogen bonds : angle 5.25558 ( 1041) link_NAG-ASN : bond 0.01387 ( 1) link_NAG-ASN : angle 1.94916 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.84 seconds wall clock time: 30 minutes 8.06 seconds (1808.06 seconds total)