Starting phenix.real_space_refine on Thu Jul 2 00:25:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7the_25893/07_2026/7the_25893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7the_25893/07_2026/7the_25893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7the_25893/07_2026/7the_25893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7the_25893/07_2026/7the_25893.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7the_25893/07_2026/7the_25893.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7the_25893/07_2026/7the_25893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7the_25893/07_2026/7the_25893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7the_25893/07_2026/7the_25893.map" } resolution = 3.87 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= -0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1543 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2098 2.51 5 N 549 2.21 5 O 641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 3305 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "B" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.92, per 1000 atoms: 0.28 Number of scatterers: 3305 At special positions: 0 Unit cell: (65.596, 81.466, 87.814, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 641 8.00 N 549 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.01 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 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 601 " - " ASN A 343 " Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 128.0 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 12.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.981A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.706A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.854A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 335 removed outlier: 7.513A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.975A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.378A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 34 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.378A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.730A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 252 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: 0.29 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 928 1.33 - 1.45: 657 1.45 - 1.57: 1781 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3388 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" CZ ARG B 94 " pdb=" NH2 ARG B 94 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" CZ ARG A 509 " pdb=" NH2 ARG A 509 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" CZ ARG A 457 " pdb=" NH2 ARG A 457 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG A 357 " pdb=" NH2 ARG A 357 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 3383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3171 1.82 - 3.63: 1161 3.63 - 5.45: 247 5.45 - 7.26: 22 7.26 - 9.08: 4 Bond angle restraints: 4605 Sorted by residual: angle pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " pdb=" CG PHE A 347 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" N CYS A 361 " pdb=" CA CYS A 361 " pdb=" C CYS A 361 " ideal model delta sigma weight residual 108.79 117.19 -8.40 1.53e+00 4.27e-01 3.01e+01 angle pdb=" C THR A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 121.75 130.83 -9.08 1.73e+00 3.34e-01 2.75e+01 angle pdb=" CA ASP A 405 " pdb=" CB ASP A 405 " pdb=" CG ASP A 405 " ideal model delta sigma weight residual 112.60 117.25 -4.65 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA ASP C 70 " pdb=" CB ASP C 70 " pdb=" CG ASP C 70 " ideal model delta sigma weight residual 112.60 117.16 -4.56 1.00e+00 1.00e+00 2.08e+01 ... (remaining 4600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1822 16.95 - 33.89: 139 33.89 - 50.84: 29 50.84 - 67.79: 7 67.79 - 84.73: 4 Dihedral angle restraints: 2001 sinusoidal: 773 harmonic: 1228 Sorted by residual: dihedral pdb=" CA ARG B 83 " pdb=" C ARG B 83 " pdb=" N SER B 84 " pdb=" CA SER B 84 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA TYR B 32 " pdb=" C TYR B 32 " pdb=" N ALA B 33 " pdb=" CA ALA B 33 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N CYS B 92 " pdb=" CA CYS B 92 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 270 0.076 - 0.152: 164 0.152 - 0.228: 49 0.228 - 0.303: 10 0.303 - 0.379: 6 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA ALA A 520 " pdb=" N ALA A 520 " pdb=" C ALA A 520 " pdb=" CB ALA A 520 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ARG B 83 " pdb=" N ARG B 83 " pdb=" C ARG B 83 " pdb=" CB ARG B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA LEU A 455 " pdb=" N LEU A 455 " pdb=" C LEU A 455 " pdb=" CB LEU A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 496 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.113 2.00e-02 2.50e+03 5.99e-02 8.96e+01 pdb=" CG TRP B 47 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.087 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 103 " 0.104 2.00e-02 2.50e+03 5.15e-02 6.64e+01 pdb=" CG TRP B 103 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 103 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 103 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 103 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 103 " -0.070 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 103 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 103 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP B 103 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.102 2.00e-02 2.50e+03 5.49e-02 6.03e+01 pdb=" CG TYR A 351 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " 0.085 2.00e-02 2.50e+03 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1818 3.02 - 3.49: 3232 3.49 - 3.96: 5382 3.96 - 4.43: 5919 4.43 - 4.90: 9826 Nonbonded interactions: 26177 Sorted by model distance: nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.548 3.040 nonbonded pdb=" OD1 ASP A 467 " pdb=" OG SER A 469 " model vdw 2.565 3.040 nonbonded pdb=" OE2 GLU A 484 " pdb=" OH TYR B 95 " model vdw 2.566 3.040 nonbonded pdb=" OH TYR B 100B" pdb=" OD1 ASN C 34 " model vdw 2.569 3.040 nonbonded pdb=" OE2 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.588 3.040 ... (remaining 26172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.580 Find NCS groups from input model: 0.010 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.013 0.069 3395 Z= 0.746 Angle : 1.878 9.080 4620 Z= 1.233 Chirality : 0.106 0.379 499 Planarity : 0.015 0.104 594 Dihedral : 13.729 84.731 1205 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.01 (0.39), residues: 417 helix: -4.02 (0.48), residues: 40 sheet: 0.21 (0.50), residues: 117 loop : -1.70 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 346 TYR 0.102 0.022 TYR A 351 PHE 0.062 0.013 PHE B 54 TRP 0.113 0.029 TRP B 47 HIS 0.007 0.004 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.01303 / 0.75 ( 3388) covalent geometry : angle 1.87726 / 1.23 ( 4605) SS BOND : bond 0.01072 / 0.81 ( 6) SS BOND : angle 1.28223 / 0.76 ( 12) hydrogen bonds : bond 0.17838 / 10.97 ( 107) hydrogen bonds : angle 8.01727 / 5.63 ( 252) link_NAG-ASN : bond 0.01889 / 0.99 ( 1) link_NAG-ASN : angle 4.19601 / 2.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7767 (p-90) cc_final: 0.7518 (p-90) REVERT: A 484 GLU cc_start: 0.8295 (pm20) cc_final: 0.7880 (pm20) REVERT: A 493 GLN cc_start: 0.8765 (tt0) cc_final: 0.8363 (tt0) REVERT: A 506 GLN cc_start: 0.7602 (mt0) cc_final: 0.7191 (mt0) REVERT: B 36 TRP cc_start: 0.9068 (m100) cc_final: 0.8251 (m-10) REVERT: B 48 MET cc_start: 0.8169 (mtp) cc_final: 0.7521 (mtm) REVERT: B 56 ILE cc_start: 0.8594 (mt) cc_final: 0.8363 (tt) REVERT: B 105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8165 (pt0) REVERT: C 34 ASN cc_start: 0.8908 (m-40) cc_final: 0.7510 (m-40) REVERT: C 89 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7011 (tm-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0770 time to fit residues: 11.4450 Evaluate side-chains 91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN B 58 ASN B 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.102980 restraints weight = 8901.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105880 restraints weight = 4652.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107789 restraints weight = 2882.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109084 restraints weight = 2000.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109730 restraints weight = 1514.301| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3395 Z= 0.163 Angle : 0.721 6.183 4620 Z= 0.389 Chirality : 0.047 0.167 499 Planarity : 0.005 0.035 594 Dihedral : 6.761 31.431 468 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.05 % Allowed : 13.02 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.49 (0.39), residues: 417 helix: -3.35 (0.69), residues: 35 sheet: 0.08 (0.45), residues: 138 loop : -1.28 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 50 TYR 0.021 0.002 TYR A 365 PHE 0.020 0.002 PHE C 98 TRP 0.015 0.002 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 3388) covalent geometry : angle 0.71758 / 0.39 ( 4605) SS BOND : bond 0.00338 / 0.21 ( 6) SS BOND : angle 1.03709 / 0.63 ( 12) hydrogen bonds : bond 0.04076 / 2.50 ( 107) hydrogen bonds : angle 6.30479 / 4.52 ( 252) link_NAG-ASN : bond 0.00124 / 0.07 ( 1) link_NAG-ASN : angle 2.23347 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7125 (ttp-110) REVERT: A 406 GLU cc_start: 0.8385 (pt0) cc_final: 0.7398 (pt0) REVERT: A 467 ASP cc_start: 0.7500 (t0) cc_final: 0.6396 (p0) REVERT: A 468 ILE cc_start: 0.9140 (pt) cc_final: 0.8907 (pt) REVERT: A 484 GLU cc_start: 0.8092 (pm20) cc_final: 0.7856 (pm20) REVERT: B 36 TRP cc_start: 0.8984 (m100) cc_final: 0.8041 (m-10) REVERT: B 48 MET cc_start: 0.8132 (mtp) cc_final: 0.7528 (mtm) REVERT: B 96 MET cc_start: 0.8084 (mtp) cc_final: 0.7752 (mmm) REVERT: B 105 GLN cc_start: 0.8718 (tt0) cc_final: 0.8142 (pt0) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.0703 time to fit residues: 8.6539 Evaluate side-chains 94 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 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 = 0.3677 r_free = 0.3677 target = 0.116185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104089 restraints weight = 8636.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107043 restraints weight = 4376.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108948 restraints weight = 2655.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110197 restraints weight = 1812.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111066 restraints weight = 1365.483| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3395 Z= 0.151 Angle : 0.633 6.228 4620 Z= 0.339 Chirality : 0.045 0.159 499 Planarity : 0.005 0.045 594 Dihedral : 5.995 32.768 468 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.43 % Allowed : 14.96 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.17 (0.40), residues: 417 helix: -2.87 (0.71), residues: 41 sheet: 0.12 (0.42), residues: 149 loop : -0.96 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 50 TYR 0.014 0.002 TYR A 365 PHE 0.008 0.001 PHE B 29 TRP 0.011 0.002 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 3388) covalent geometry : angle 0.63023 / 0.34 ( 4605) SS BOND : bond 0.00293 / 0.19 ( 6) SS BOND : angle 0.85949 / 0.52 ( 12) hydrogen bonds : bond 0.03689 / 2.33 ( 107) hydrogen bonds : angle 6.09179 / 4.37 ( 252) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 1.86149 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7686 (m110) cc_final: 0.7262 (m110) REVERT: A 467 ASP cc_start: 0.7350 (t0) cc_final: 0.6379 (p0) REVERT: B 36 TRP cc_start: 0.9022 (m100) cc_final: 0.8169 (m-10) REVERT: B 48 MET cc_start: 0.8114 (mtp) cc_final: 0.7346 (mtm) REVERT: B 61 GLN cc_start: 0.8881 (pm20) cc_final: 0.8357 (pp30) REVERT: B 96 MET cc_start: 0.8221 (mtp) cc_final: 0.7969 (mmm) REVERT: B 105 GLN cc_start: 0.8672 (tt0) cc_final: 0.8237 (pt0) REVERT: C 89 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7453 (tm-30) outliers start: 16 outliers final: 13 residues processed: 104 average time/residue: 0.0742 time to fit residues: 9.2223 Evaluate side-chains 99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 55 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 = 0.3709 r_free = 0.3709 target = 0.117861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.105738 restraints weight = 8615.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108596 restraints weight = 4467.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110466 restraints weight = 2758.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.111751 restraints weight = 1913.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.112621 restraints weight = 1442.160| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3395 Z= 0.120 Angle : 0.603 5.652 4620 Z= 0.323 Chirality : 0.044 0.171 499 Planarity : 0.005 0.045 594 Dihedral : 5.603 28.743 468 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.43 % Allowed : 16.62 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.83 (0.42), residues: 417 helix: -2.67 (0.75), residues: 41 sheet: 0.29 (0.42), residues: 150 loop : -0.67 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 50 TYR 0.016 0.001 TYR A 451 PHE 0.007 0.001 PHE C 62 TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3388) covalent geometry : angle 0.60159 / 0.32 ( 4605) SS BOND : bond 0.00255 / 0.15 ( 6) SS BOND : angle 0.82661 / 0.49 ( 12) hydrogen bonds : bond 0.03344 / 2.14 ( 107) hydrogen bonds : angle 5.93826 / 4.30 ( 252) link_NAG-ASN : bond 0.00118 / 0.06 ( 1) link_NAG-ASN : angle 1.57777 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7672 (m110) cc_final: 0.7213 (m110) REVERT: A 467 ASP cc_start: 0.7084 (t0) cc_final: 0.6392 (p0) REVERT: B 36 TRP cc_start: 0.8937 (m100) cc_final: 0.8185 (m-10) REVERT: B 48 MET cc_start: 0.8128 (mtp) cc_final: 0.7414 (mtm) REVERT: B 99 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8528 (tmm-80) REVERT: B 105 GLN cc_start: 0.8702 (tt0) cc_final: 0.8199 (pt0) REVERT: C 31 ASN cc_start: 0.7852 (m-40) cc_final: 0.7160 (t0) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.0695 time to fit residues: 8.3673 Evaluate side-chains 95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.118121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.106021 restraints weight = 8694.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108831 restraints weight = 4474.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110706 restraints weight = 2767.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111917 restraints weight = 1919.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.112781 restraints weight = 1462.810| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3395 Z= 0.118 Angle : 0.602 7.135 4620 Z= 0.318 Chirality : 0.044 0.187 499 Planarity : 0.005 0.047 594 Dihedral : 5.326 27.200 468 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.26 % Allowed : 16.34 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.85 (0.41), residues: 417 helix: -2.69 (0.74), residues: 41 sheet: 0.27 (0.42), residues: 151 loop : -0.67 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 403 TYR 0.011 0.001 TYR B 100C PHE 0.009 0.001 PHE C 62 TRP 0.008 0.001 TRP B 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 3388) covalent geometry : angle 0.59998 / 0.32 ( 4605) SS BOND : bond 0.00215 / 0.14 ( 6) SS BOND : angle 0.83351 / 0.49 ( 12) hydrogen bonds : bond 0.03240 / 2.07 ( 107) hydrogen bonds : angle 5.86680 / 4.27 ( 252) link_NAG-ASN : bond 0.00115 / 0.06 ( 1) link_NAG-ASN : angle 1.50730 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7690 (m110) cc_final: 0.7254 (m110) REVERT: A 423 TYR cc_start: 0.7665 (t80) cc_final: 0.7461 (t80) REVERT: A 467 ASP cc_start: 0.7025 (t0) cc_final: 0.6214 (p0) REVERT: B 36 TRP cc_start: 0.8948 (m100) cc_final: 0.8487 (m100) REVERT: B 48 MET cc_start: 0.8113 (mtp) cc_final: 0.7413 (mtm) REVERT: B 82 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7048 (pp) REVERT: B 99 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8799 (tmm-80) REVERT: B 100 ASP cc_start: 0.8484 (p0) cc_final: 0.8137 (p0) REVERT: B 105 GLN cc_start: 0.8642 (tt0) cc_final: 0.8159 (pt0) REVERT: C 31 ASN cc_start: 0.7757 (m-40) cc_final: 0.7231 (t0) REVERT: C 89 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7500 (tm-30) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.0665 time to fit residues: 8.0617 Evaluate side-chains 96 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.116295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.104228 restraints weight = 8731.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107015 restraints weight = 4496.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.108869 restraints weight = 2780.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110019 restraints weight = 1931.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110889 restraints weight = 1485.656| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3395 Z= 0.146 Angle : 0.616 6.334 4620 Z= 0.328 Chirality : 0.044 0.174 499 Planarity : 0.005 0.049 594 Dihedral : 5.380 26.270 468 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.54 % Allowed : 17.73 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.85 (0.42), residues: 417 helix: -2.69 (0.74), residues: 41 sheet: 0.31 (0.42), residues: 148 loop : -0.69 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.011 0.001 TYR A 451 PHE 0.008 0.001 PHE C 62 TRP 0.011 0.002 TRP A 353 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 3388) covalent geometry : angle 0.61405 / 0.33 ( 4605) SS BOND : bond 0.00262 / 0.17 ( 6) SS BOND : angle 0.87945 / 0.52 ( 12) hydrogen bonds : bond 0.03352 / 2.14 ( 107) hydrogen bonds : angle 5.93799 / 4.33 ( 252) link_NAG-ASN : bond 0.00054 / 0.03 ( 1) link_NAG-ASN : angle 1.68413 / 0.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7764 (m110) cc_final: 0.7306 (m110) REVERT: A 423 TYR cc_start: 0.7651 (t80) cc_final: 0.7390 (t80) REVERT: A 467 ASP cc_start: 0.7098 (t70) cc_final: 0.6315 (p0) REVERT: A 493 GLN cc_start: 0.8744 (tt0) cc_final: 0.8465 (tt0) REVERT: B 36 TRP cc_start: 0.9040 (m100) cc_final: 0.8669 (m100) REVERT: B 82 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7048 (pp) REVERT: B 96 MET cc_start: 0.8445 (mmm) cc_final: 0.8236 (mmm) REVERT: B 99 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8821 (tmm-80) REVERT: B 100 ASP cc_start: 0.8385 (p0) cc_final: 0.8035 (p0) REVERT: B 105 GLN cc_start: 0.8649 (tt0) cc_final: 0.8174 (pt0) REVERT: C 89 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 20 outliers final: 17 residues processed: 103 average time/residue: 0.0619 time to fit residues: 7.8681 Evaluate side-chains 101 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0010 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.118215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.106004 restraints weight = 8813.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108837 restraints weight = 4518.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110672 restraints weight = 2778.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.111865 restraints weight = 1935.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112735 restraints weight = 1480.089| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3395 Z= 0.120 Angle : 0.584 5.658 4620 Z= 0.313 Chirality : 0.043 0.154 499 Planarity : 0.005 0.050 594 Dihedral : 5.197 25.695 468 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.71 % Allowed : 19.11 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.93 (0.41), residues: 417 helix: -3.17 (0.63), residues: 41 sheet: 0.22 (0.42), residues: 149 loop : -0.63 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 50 TYR 0.010 0.001 TYR A 423 PHE 0.008 0.001 PHE C 62 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3388) covalent geometry : angle 0.58063 / 0.31 ( 4605) SS BOND : bond 0.00225 / 0.14 ( 6) SS BOND : angle 1.11529 / 0.71 ( 12) hydrogen bonds : bond 0.03191 / 2.06 ( 107) hydrogen bonds : angle 5.96688 / 4.40 ( 252) link_NAG-ASN : bond 0.00093 / 0.05 ( 1) link_NAG-ASN : angle 1.53760 / 0.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7768 (m110) cc_final: 0.7307 (m110) REVERT: A 423 TYR cc_start: 0.7606 (t80) cc_final: 0.7391 (t80) REVERT: A 467 ASP cc_start: 0.7074 (t70) cc_final: 0.6338 (p0) REVERT: A 493 GLN cc_start: 0.8739 (tt0) cc_final: 0.8494 (tt0) REVERT: B 36 TRP cc_start: 0.8997 (m100) cc_final: 0.8440 (m-10) REVERT: B 82 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7047 (pp) REVERT: B 96 MET cc_start: 0.8482 (mmm) cc_final: 0.8210 (mmm) REVERT: B 99 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8785 (tmm-80) REVERT: B 100 ASP cc_start: 0.8213 (p0) cc_final: 0.7821 (p0) REVERT: B 105 GLN cc_start: 0.8675 (tt0) cc_final: 0.8202 (pt0) REVERT: C 31 ASN cc_start: 0.7604 (m-40) cc_final: 0.7058 (t0) outliers start: 17 outliers final: 14 residues processed: 96 average time/residue: 0.0615 time to fit residues: 7.2611 Evaluate side-chains 99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 38 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.117141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105085 restraints weight = 8780.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107915 restraints weight = 4482.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109764 restraints weight = 2736.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110986 restraints weight = 1892.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.111780 restraints weight = 1430.840| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3395 Z= 0.134 Angle : 0.594 5.913 4620 Z= 0.319 Chirality : 0.044 0.150 499 Planarity : 0.005 0.051 594 Dihedral : 5.250 26.086 468 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.26 % Allowed : 17.73 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.99 (0.41), residues: 417 helix: -3.11 (0.65), residues: 41 sheet: 0.20 (0.41), residues: 155 loop : -0.73 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 403 TYR 0.010 0.001 TYR A 423 PHE 0.008 0.001 PHE C 62 TRP 0.011 0.002 TRP B 47 HIS 0.002 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3388) covalent geometry : angle 0.59084 / 0.32 ( 4605) SS BOND : bond 0.00232 / 0.15 ( 6) SS BOND : angle 1.15833 / 0.74 ( 12) hydrogen bonds : bond 0.03367 / 2.10 ( 107) hydrogen bonds : angle 6.03975 / 4.46 ( 252) link_NAG-ASN : bond 0.00065 / 0.03 ( 1) link_NAG-ASN : angle 1.58687 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7738 (m110) cc_final: 0.7324 (m110) REVERT: A 423 TYR cc_start: 0.7546 (t80) cc_final: 0.7336 (t80) REVERT: A 467 ASP cc_start: 0.7149 (t70) cc_final: 0.6406 (p0) REVERT: A 509 ARG cc_start: 0.8129 (mtt180) cc_final: 0.6797 (mtt90) REVERT: B 36 TRP cc_start: 0.9026 (m100) cc_final: 0.8631 (m-10) REVERT: B 48 MET cc_start: 0.8276 (mtp) cc_final: 0.8059 (mtp) REVERT: B 82 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7029 (pp) REVERT: B 99 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8732 (tmm-80) REVERT: B 100 ASP cc_start: 0.8192 (p0) cc_final: 0.7843 (p0) REVERT: B 105 GLN cc_start: 0.8687 (tt0) cc_final: 0.8200 (pt0) REVERT: C 31 ASN cc_start: 0.7612 (m-40) cc_final: 0.7087 (t0) outliers start: 19 outliers final: 16 residues processed: 98 average time/residue: 0.0669 time to fit residues: 7.9775 Evaluate side-chains 102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.0050 chunk 37 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.117699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.105381 restraints weight = 8794.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108192 restraints weight = 4562.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.110051 restraints weight = 2820.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111238 restraints weight = 1964.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112147 restraints weight = 1512.473| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3395 Z= 0.135 Angle : 0.611 6.196 4620 Z= 0.327 Chirality : 0.044 0.155 499 Planarity : 0.005 0.052 594 Dihedral : 5.217 26.328 468 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.99 % Allowed : 17.73 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.00 (0.41), residues: 417 helix: -3.13 (0.66), residues: 41 sheet: 0.17 (0.42), residues: 149 loop : -0.69 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 94 TYR 0.011 0.001 TYR B 95 PHE 0.008 0.001 PHE C 62 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 3388) covalent geometry : angle 0.60818 / 0.33 ( 4605) SS BOND : bond 0.00215 / 0.14 ( 6) SS BOND : angle 1.14358 / 0.73 ( 12) hydrogen bonds : bond 0.03277 / 2.06 ( 107) hydrogen bonds : angle 5.83388 / 4.27 ( 252) link_NAG-ASN : bond 0.00087 / 0.05 ( 1) link_NAG-ASN : angle 1.54841 / 0.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7727 (m110) cc_final: 0.7278 (m110) REVERT: A 403 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7492 (ttp-110) REVERT: A 423 TYR cc_start: 0.7591 (t80) cc_final: 0.7382 (t80) REVERT: A 467 ASP cc_start: 0.7150 (t70) cc_final: 0.6438 (p0) REVERT: B 36 TRP cc_start: 0.9064 (m100) cc_final: 0.8651 (m-10) REVERT: B 48 MET cc_start: 0.8231 (mtp) cc_final: 0.7943 (mtp) REVERT: B 82 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7046 (pp) REVERT: B 99 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8787 (tmm-80) REVERT: B 100 ASP cc_start: 0.8163 (p0) cc_final: 0.7847 (p0) REVERT: B 105 GLN cc_start: 0.8687 (tt0) cc_final: 0.8165 (pt0) REVERT: C 31 ASN cc_start: 0.7518 (m-40) cc_final: 0.7054 (t0) outliers start: 18 outliers final: 16 residues processed: 94 average time/residue: 0.0573 time to fit residues: 6.7897 Evaluate side-chains 100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.115564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103254 restraints weight = 8798.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106101 restraints weight = 4557.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107934 restraints weight = 2808.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109181 restraints weight = 1954.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.109988 restraints weight = 1481.888| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3395 Z= 0.173 Angle : 0.636 6.429 4620 Z= 0.342 Chirality : 0.045 0.153 499 Planarity : 0.005 0.050 594 Dihedral : 5.512 26.762 468 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.26 % Allowed : 18.28 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.15 (0.41), residues: 417 helix: -3.08 (0.66), residues: 41 sheet: 0.05 (0.41), residues: 153 loop : -0.83 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 94 TYR 0.019 0.002 TYR C 92 PHE 0.009 0.001 PHE A 464 TRP 0.010 0.002 TRP B 47 HIS 0.004 0.003 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 3388) covalent geometry : angle 0.63181 / 0.34 ( 4605) SS BOND : bond 0.00285 / 0.19 ( 6) SS BOND : angle 1.28375 / 0.82 ( 12) hydrogen bonds : bond 0.03567 / 2.24 ( 107) hydrogen bonds : angle 5.91663 / 4.33 ( 252) link_NAG-ASN : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : angle 1.81357 / 1.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7817 (m110) cc_final: 0.7395 (m110) REVERT: A 403 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7496 (ttp-110) REVERT: A 405 ASP cc_start: 0.7749 (p0) cc_final: 0.7443 (p0) REVERT: A 423 TYR cc_start: 0.7606 (t80) cc_final: 0.7388 (t80) REVERT: A 467 ASP cc_start: 0.7320 (t70) cc_final: 0.6523 (p0) REVERT: B 48 MET cc_start: 0.8261 (mtp) cc_final: 0.7960 (mtp) REVERT: B 82 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7199 (pp) REVERT: B 99 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8807 (tmm-80) REVERT: B 100 ASP cc_start: 0.8261 (p0) cc_final: 0.7940 (p0) REVERT: B 105 GLN cc_start: 0.8748 (tt0) cc_final: 0.8204 (pt0) REVERT: C 31 ASN cc_start: 0.7580 (m-40) cc_final: 0.7049 (t0) REVERT: C 89 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7782 (tm-30) outliers start: 19 outliers final: 16 residues processed: 92 average time/residue: 0.0584 time to fit residues: 6.7616 Evaluate side-chains 98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.117507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.105158 restraints weight = 8856.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107979 restraints weight = 4595.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109823 restraints weight = 2841.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111059 restraints weight = 1981.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.111856 restraints weight = 1512.547| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3395 Z= 0.136 Angle : 0.614 6.310 4620 Z= 0.330 Chirality : 0.044 0.156 499 Planarity : 0.005 0.052 594 Dihedral : 5.328 26.092 468 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.71 % Allowed : 19.11 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.12 (0.41), residues: 417 helix: -3.03 (0.67), residues: 41 sheet: 0.12 (0.42), residues: 152 loop : -0.86 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 94 TYR 0.019 0.001 TYR C 92 PHE 0.008 0.001 PHE C 62 TRP 0.011 0.001 TRP B 47 HIS 0.002 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 3388) covalent geometry : angle 0.61049 / 0.33 ( 4605) SS BOND : bond 0.00227 / 0.15 ( 6) SS BOND : angle 1.17343 / 0.75 ( 12) hydrogen bonds : bond 0.03343 / 2.12 ( 107) hydrogen bonds : angle 5.83428 / 4.29 ( 252) link_NAG-ASN : bond 0.00063 / 0.03 ( 1) link_NAG-ASN : angle 1.59612 / 0.90 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 864.27 seconds wall clock time: 15 minutes 33.69 seconds (933.69 seconds total)