Starting phenix.real_space_refine on Tue Aug 4 14:10:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yx7_73597/08_2026/9yx7_73597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yx7_73597/08_2026/9yx7_73597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yx7_73597/08_2026/9yx7_73597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yx7_73597/08_2026/9yx7_73597.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yx7_73597/08_2026/9yx7_73597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yx7_73597/08_2026/9yx7_73597.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2348 2.51 5 N 584 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3609 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1847 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 14, 'TRANS': 215} Chain: "C" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1678 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.04, per 1000 atoms: 0.29 Number of scatterers: 3609 At special positions: 0 Unit cell: (75.712, 82.368, 84.864, 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 12 16.00 O 665 8.00 N 584 7.00 C 2348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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 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 A1301 " - " ASN A 529 " " NAG A1302 " - " ASN A 331 " " NAG C1301 " - " ASN C 281 " " NAG C1302 " - " ASN C 233 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 122 " Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 77.8 milliseconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 820 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.580A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.936A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.556A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 327 removed outlier: 7.078A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.030A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.757A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.662A pdb=" N ASN C 61 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR C 268 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE C 201 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP C 227 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE C 203 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 55 Processing sheet with id=AA7, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.408A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 264 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: 0.50 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1097 1.34 - 1.46: 998 1.46 - 1.58: 1606 1.58 - 1.70: 0 1.70 - 1.82: 13 Bond restraints: 3714 Sorted by residual: bond pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.21e-02 6.83e+03 7.26e+00 bond pdb=" N HIS C 66 " pdb=" CA HIS C 66 " ideal model delta sigma weight residual 1.454 1.478 -0.024 1.21e-02 6.83e+03 3.89e+00 bond pdb=" CG HIS C 66 " pdb=" CD2 HIS C 66 " ideal model delta sigma weight residual 1.354 1.338 0.016 1.10e-02 8.26e+03 2.24e+00 bond pdb=" CB GLN A 474 " pdb=" CG GLN A 474 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" CB ASP A 428 " pdb=" CG ASP A 428 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.82e+00 ... (remaining 3709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 4938 1.76 - 3.52: 89 3.52 - 5.29: 22 5.29 - 7.05: 2 7.05 - 8.81: 1 Bond angle restraints: 5052 Sorted by residual: angle pdb=" N GLN A 474 " pdb=" CA GLN A 474 " pdb=" C GLN A 474 " ideal model delta sigma weight residual 108.76 114.35 -5.59 1.58e+00 4.01e-01 1.25e+01 angle pdb=" CA GLN C 173 " pdb=" CB GLN C 173 " pdb=" CG GLN C 173 " ideal model delta sigma weight residual 114.10 119.67 -5.57 2.00e+00 2.50e-01 7.75e+00 angle pdb=" CA GLU C 169 " pdb=" CB GLU C 169 " pdb=" CG GLU C 169 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 6.99e+00 angle pdb=" CA ILE A 418 " pdb=" C ILE A 418 " pdb=" O ILE A 418 " ideal model delta sigma weight residual 120.85 118.08 2.77 1.06e+00 8.90e-01 6.82e+00 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 113.76 118.37 -4.61 1.80e+00 3.09e-01 6.56e+00 ... (remaining 5047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.06: 1934 14.06 - 28.12: 204 28.12 - 42.18: 77 42.18 - 56.24: 21 56.24 - 70.30: 3 Dihedral angle restraints: 2239 sinusoidal: 962 harmonic: 1277 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 121.04 -28.04 1 1.00e+01 1.00e-02 1.13e+01 dihedral pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " ideal model delta sinusoidal sigma weight residual -73.00 -17.41 -55.59 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CG ARG A 328 " pdb=" CD ARG A 328 " pdb=" NE ARG A 328 " pdb=" CZ ARG A 328 " ideal model delta sinusoidal sigma weight residual -90.00 -133.18 43.18 2 1.50e+01 4.44e-03 9.99e+00 ... (remaining 2236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 382 0.040 - 0.081: 113 0.081 - 0.121: 60 0.121 - 0.162: 4 0.162 - 0.202: 2 Chirality restraints: 561 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE A 418 " pdb=" N ILE A 418 " pdb=" C ILE A 418 " pdb=" CB ILE A 418 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 281 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 558 not shown) Planarity restraints: 645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 474 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" CD GLN A 474 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN A 474 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 474 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 280 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" CD GLU C 280 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU C 280 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 280 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 111 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" CG ASP C 111 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP C 111 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP C 111 " -0.009 2.00e-02 2.50e+03 ... (remaining 642 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1923 2.99 - 3.47: 3162 3.47 - 3.95: 5602 3.95 - 4.42: 6471 4.42 - 4.90: 10633 Nonbonded interactions: 27791 Sorted by model distance: nonbonded pdb=" O THR C 124 " pdb=" OG1 THR C 124 " model vdw 2.517 3.040 nonbonded pdb=" N THR C 187 " pdb=" OG1 THR C 187 " model vdw 2.551 2.496 nonbonded pdb=" N GLU C 132 " pdb=" OE1 GLU C 132 " model vdw 2.587 3.120 nonbonded pdb=" N VAL C 130 " pdb=" N CYS C 131 " model vdw 2.613 2.560 nonbonded pdb=" N ASP A 398 " pdb=" OD1 ASP A 398 " model vdw 2.614 3.120 ... (remaining 27786 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: 6.030 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.190 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.003 0.041 3724 Z= 0.144 Angle : 0.624 8.811 5078 Z= 0.328 Chirality : 0.047 0.202 561 Planarity : 0.003 0.032 639 Dihedral : 13.868 70.297 1407 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.51 % Allowed : 23.53 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.41), residues: 422 helix: -3.41 (0.58), residues: 20 sheet: 0.42 (0.53), residues: 109 loop : -0.89 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 213 TYR 0.013 0.001 TYR A 489 PHE 0.014 0.001 PHE C 172 TRP 0.008 0.001 TRP C 104 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 3714) covalent geometry : angle 0.61313 / 0.33 ( 5052) SS BOND : bond 0.00238 / 0.14 ( 4) SS BOND : angle 1.07401 / 0.67 ( 8) hydrogen bonds : bond 0.18303 / 12.31 ( 107) hydrogen bonds : angle 9.72032 / 6.63 ( 264) link_NAG-ASN : bond 0.00344 / 0.19 ( 6) link_NAG-ASN : angle 1.97436 / 1.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASN cc_start: 0.7758 (m110) cc_final: 0.7191 (t0) REVERT: A 496 SER cc_start: 0.8496 (m) cc_final: 0.8009 (t) REVERT: A 535 LYS cc_start: 0.9044 (mttt) cc_final: 0.6536 (tptm) REVERT: A 537 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8031 (mtpp) REVERT: C 52 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8739 (tm-30) REVERT: C 172 PHE cc_start: 0.6946 (t80) cc_final: 0.6721 (t80) REVERT: C 214 ASP cc_start: 0.8411 (m-30) cc_final: 0.8131 (m-30) outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.6834 time to fit residues: 51.8346 Evaluate side-chains 56 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 187 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.100360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073237 restraints weight = 6846.703| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.42 r_work: 0.2910 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3724 Z= 0.134 Angle : 0.535 7.971 5078 Z= 0.271 Chirality : 0.045 0.197 561 Planarity : 0.004 0.032 639 Dihedral : 6.349 56.277 602 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.60 % Allowed : 23.02 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.41), residues: 422 helix: -3.23 (0.64), residues: 21 sheet: 0.42 (0.51), residues: 116 loop : -0.83 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 213 TYR 0.012 0.001 TYR A 489 PHE 0.014 0.001 PHE C 133 TRP 0.013 0.001 TRP C 64 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 3714) covalent geometry : angle 0.52251 / 0.27 ( 5052) SS BOND : bond 0.00157 / 0.10 ( 4) SS BOND : angle 0.81576 / 0.54 ( 8) hydrogen bonds : bond 0.03509 / 2.39 ( 107) hydrogen bonds : angle 6.84308 / 4.70 ( 264) link_NAG-ASN : bond 0.00239 / 0.13 ( 6) link_NAG-ASN : angle 1.99107 / 1.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8753 (tt0) cc_final: 0.8445 (tt0) REVERT: A 417 ASN cc_start: 0.7782 (m110) cc_final: 0.7435 (t0) REVERT: A 438 SER cc_start: 0.8602 (t) cc_final: 0.8123 (t) REVERT: A 448 ASN cc_start: 0.6398 (OUTLIER) cc_final: 0.5807 (m-40) REVERT: A 496 SER cc_start: 0.8496 (m) cc_final: 0.7988 (t) REVERT: C 52 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8815 (tm-30) REVERT: C 172 PHE cc_start: 0.6966 (t80) cc_final: 0.6720 (t80) REVERT: C 214 ASP cc_start: 0.8412 (m-30) cc_final: 0.8075 (m-30) outliers start: 18 outliers final: 8 residues processed: 70 average time/residue: 0.5635 time to fit residues: 40.5981 Evaluate side-chains 59 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.071897 restraints weight = 6581.054| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.31 r_work: 0.2898 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3724 Z= 0.186 Angle : 0.558 6.542 5078 Z= 0.283 Chirality : 0.047 0.208 561 Planarity : 0.004 0.032 639 Dihedral : 6.359 55.840 602 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.09 % Allowed : 22.76 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.41), residues: 422 helix: -3.13 (0.69), residues: 21 sheet: 0.42 (0.49), residues: 116 loop : -0.85 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 213 TYR 0.014 0.001 TYR A 489 PHE 0.012 0.001 PHE C 86 TRP 0.012 0.002 TRP C 64 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 3714) covalent geometry : angle 0.54448 / 0.28 ( 5052) SS BOND : bond 0.00155 / 0.10 ( 4) SS BOND : angle 0.78446 / 0.53 ( 8) hydrogen bonds : bond 0.03316 / 2.24 ( 107) hydrogen bonds : angle 6.31231 / 4.32 ( 264) link_NAG-ASN : bond 0.00176 / 0.09 ( 6) link_NAG-ASN : angle 2.08982 / 1.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.6385 (OUTLIER) cc_final: 0.5686 (m-40) REVERT: A 496 SER cc_start: 0.8501 (m) cc_final: 0.8018 (t) REVERT: C 52 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8839 (tm-30) REVERT: C 172 PHE cc_start: 0.7011 (t80) cc_final: 0.6804 (t80) REVERT: C 186 PHE cc_start: 0.6409 (p90) cc_final: 0.5826 (p90) REVERT: C 214 ASP cc_start: 0.8411 (m-30) cc_final: 0.8067 (m-30) REVERT: C 217 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8575 (mm-40) outliers start: 16 outliers final: 9 residues processed: 70 average time/residue: 0.5654 time to fit residues: 40.8809 Evaluate side-chains 65 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 2 optimal weight: 0.1980 chunk 20 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.100657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073476 restraints weight = 6603.553| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.34 r_work: 0.2914 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3724 Z= 0.108 Angle : 0.531 5.991 5078 Z= 0.272 Chirality : 0.046 0.201 561 Planarity : 0.003 0.030 639 Dihedral : 6.210 56.446 602 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.07 % Allowed : 22.51 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.40), residues: 422 helix: -2.58 (0.88), residues: 21 sheet: 0.42 (0.50), residues: 110 loop : -0.86 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 213 TYR 0.014 0.001 TYR A 489 PHE 0.009 0.001 PHE C 65 TRP 0.008 0.001 TRP C 64 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 3714) covalent geometry : angle 0.51815 / 0.27 ( 5052) SS BOND : bond 0.00317 / 0.17 ( 4) SS BOND : angle 0.80636 / 0.47 ( 8) hydrogen bonds : bond 0.02815 / 1.90 ( 107) hydrogen bonds : angle 6.06579 / 4.16 ( 264) link_NAG-ASN : bond 0.00289 / 0.16 ( 6) link_NAG-ASN : angle 1.97640 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 448 ASN cc_start: 0.6340 (OUTLIER) cc_final: 0.5697 (m-40) REVERT: A 496 SER cc_start: 0.8473 (m) cc_final: 0.7989 (t) REVERT: C 52 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8800 (tm-30) REVERT: C 172 PHE cc_start: 0.6971 (t80) cc_final: 0.6689 (t80) REVERT: C 186 PHE cc_start: 0.6395 (p90) cc_final: 0.5868 (p90) REVERT: C 197 ILE cc_start: 0.9032 (tp) cc_final: 0.8768 (pp) REVERT: C 214 ASP cc_start: 0.8361 (m-30) cc_final: 0.8012 (m-30) outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 0.5811 time to fit residues: 37.7391 Evaluate side-chains 56 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 211 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.100188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.072999 restraints weight = 6719.440| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.37 r_work: 0.2906 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3724 Z= 0.118 Angle : 0.523 5.795 5078 Z= 0.266 Chirality : 0.046 0.204 561 Planarity : 0.003 0.031 639 Dihedral : 6.089 56.115 601 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.84 % Allowed : 22.51 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.40), residues: 422 helix: -2.58 (0.88), residues: 21 sheet: 0.36 (0.48), residues: 116 loop : -0.84 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.012 0.001 TYR A 489 PHE 0.009 0.001 PHE C 65 TRP 0.008 0.001 TRP C 64 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 3714) covalent geometry : angle 0.50997 / 0.26 ( 5052) SS BOND : bond 0.00154 / 0.10 ( 4) SS BOND : angle 0.74846 / 0.50 ( 8) hydrogen bonds : bond 0.02726 / 1.83 ( 107) hydrogen bonds : angle 5.91209 / 4.06 ( 264) link_NAG-ASN : bond 0.00261 / 0.15 ( 6) link_NAG-ASN : angle 1.97505 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8413 (mt-10) REVERT: A 448 ASN cc_start: 0.6253 (OUTLIER) cc_final: 0.5580 (m-40) REVERT: A 496 SER cc_start: 0.8473 (m) cc_final: 0.7993 (t) REVERT: A 519 HIS cc_start: 0.6585 (OUTLIER) cc_final: 0.6243 (m-70) REVERT: C 52 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8801 (tm-30) REVERT: C 172 PHE cc_start: 0.6945 (t80) cc_final: 0.6733 (t80) REVERT: C 186 PHE cc_start: 0.6556 (p90) cc_final: 0.6035 (p90) REVERT: C 197 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8363 (pp) REVERT: C 214 ASP cc_start: 0.8361 (m-30) cc_final: 0.8009 (m-30) REVERT: C 217 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8614 (mm-40) outliers start: 15 outliers final: 6 residues processed: 66 average time/residue: 0.5960 time to fit residues: 40.5255 Evaluate side-chains 65 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 217 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.4320 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.098133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070792 restraints weight = 6727.923| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.35 r_work: 0.2882 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3724 Z= 0.224 Angle : 0.600 5.987 5078 Z= 0.307 Chirality : 0.048 0.208 561 Planarity : 0.004 0.034 639 Dihedral : 6.273 56.305 601 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.58 % Allowed : 22.76 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.40), residues: 422 helix: -2.65 (0.85), residues: 20 sheet: 0.39 (0.48), residues: 116 loop : -0.99 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 213 TYR 0.013 0.001 TYR C 278 PHE 0.014 0.002 PHE C 86 TRP 0.010 0.002 TRP C 64 HIS 0.008 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 ( 3714) covalent geometry : angle 0.58710 / 0.30 ( 5052) SS BOND : bond 0.00242 / 0.15 ( 4) SS BOND : angle 1.03187 / 0.66 ( 8) hydrogen bonds : bond 0.03086 / 2.02 ( 107) hydrogen bonds : angle 5.99115 / 4.11 ( 264) link_NAG-ASN : bond 0.00166 / 0.09 ( 6) link_NAG-ASN : angle 2.09910 / 1.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8628 (mt-10) REVERT: A 418 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8754 (mp) REVERT: A 448 ASN cc_start: 0.6401 (OUTLIER) cc_final: 0.5639 (m-40) REVERT: A 496 SER cc_start: 0.8492 (m) cc_final: 0.8010 (t) REVERT: C 52 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8850 (tm-30) REVERT: C 186 PHE cc_start: 0.6509 (p90) cc_final: 0.6034 (p90) REVERT: C 214 ASP cc_start: 0.8393 (m-30) cc_final: 0.8046 (m-30) REVERT: C 217 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8563 (mm-40) outliers start: 14 outliers final: 6 residues processed: 68 average time/residue: 0.5873 time to fit residues: 41.1535 Evaluate side-chains 63 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 217 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.098896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.071698 restraints weight = 6790.704| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.37 r_work: 0.2880 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3724 Z= 0.149 Angle : 0.571 5.487 5078 Z= 0.291 Chirality : 0.047 0.198 561 Planarity : 0.004 0.036 639 Dihedral : 6.240 56.635 601 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.07 % Allowed : 23.53 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.40), residues: 422 helix: -2.76 (0.84), residues: 21 sheet: 0.38 (0.49), residues: 116 loop : -0.96 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 213 TYR 0.013 0.001 TYR A 489 PHE 0.019 0.001 PHE C 172 TRP 0.009 0.001 TRP C 64 HIS 0.001 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3714) covalent geometry : angle 0.55793 / 0.29 ( 5052) SS BOND : bond 0.00128 / 0.08 ( 4) SS BOND : angle 0.94565 / 0.62 ( 8) hydrogen bonds : bond 0.02811 / 1.86 ( 107) hydrogen bonds : angle 5.90730 / 4.06 ( 264) link_NAG-ASN : bond 0.00218 / 0.12 ( 6) link_NAG-ASN : angle 2.01946 / 1.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8450 (mt-10) REVERT: A 448 ASN cc_start: 0.6360 (OUTLIER) cc_final: 0.5646 (m-40) REVERT: A 496 SER cc_start: 0.8495 (m) cc_final: 0.7995 (t) REVERT: A 519 HIS cc_start: 0.6300 (OUTLIER) cc_final: 0.5939 (t-90) REVERT: C 52 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8844 (tm-30) REVERT: C 186 PHE cc_start: 0.6571 (p90) cc_final: 0.6127 (p90) REVERT: C 214 ASP cc_start: 0.8361 (m-30) cc_final: 0.8007 (m-30) REVERT: C 217 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8607 (mm-40) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.6001 time to fit residues: 38.8973 Evaluate side-chains 61 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 217 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.099346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072199 restraints weight = 6746.334| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.36 r_work: 0.2889 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3724 Z= 0.138 Angle : 0.568 5.384 5078 Z= 0.291 Chirality : 0.047 0.201 561 Planarity : 0.004 0.038 639 Dihedral : 6.166 56.470 601 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.84 % Allowed : 23.53 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.40), residues: 422 helix: -2.79 (0.83), residues: 21 sheet: 0.17 (0.46), residues: 122 loop : -0.88 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 213 TYR 0.013 0.001 TYR A 489 PHE 0.009 0.001 PHE C 86 TRP 0.008 0.001 TRP C 64 HIS 0.001 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 3714) covalent geometry : angle 0.55608 / 0.29 ( 5052) SS BOND : bond 0.00173 / 0.11 ( 4) SS BOND : angle 0.87336 / 0.58 ( 8) hydrogen bonds : bond 0.02744 / 1.82 ( 107) hydrogen bonds : angle 5.86443 / 4.02 ( 264) link_NAG-ASN : bond 0.00235 / 0.13 ( 6) link_NAG-ASN : angle 2.00866 / 1.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8436 (mt-10) REVERT: A 448 ASN cc_start: 0.6363 (OUTLIER) cc_final: 0.5652 (m-40) REVERT: A 496 SER cc_start: 0.8483 (m) cc_final: 0.7994 (t) REVERT: A 519 HIS cc_start: 0.6576 (OUTLIER) cc_final: 0.6077 (t-90) REVERT: C 52 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8824 (tm-30) REVERT: C 186 PHE cc_start: 0.6672 (p90) cc_final: 0.6241 (p90) REVERT: C 210 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8915 (pp) REVERT: C 214 ASP cc_start: 0.8344 (m-30) cc_final: 0.8001 (m-30) REVERT: C 217 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8604 (mm-40) outliers start: 15 outliers final: 7 residues processed: 68 average time/residue: 0.5798 time to fit residues: 40.6285 Evaluate side-chains 66 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 217 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 42 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 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 = 0.3510 r_free = 0.3510 target = 0.100191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073177 restraints weight = 6743.357| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.35 r_work: 0.2905 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 0.034 3724 Z= 0.122 Angle : 0.585 9.629 5078 Z= 0.293 Chirality : 0.047 0.199 561 Planarity : 0.004 0.039 639 Dihedral : 6.125 56.735 601 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.56 % Allowed : 24.55 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.40), residues: 422 helix: -2.74 (0.84), residues: 21 sheet: 0.18 (0.46), residues: 122 loop : -0.84 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 213 TYR 0.012 0.001 TYR A 489 PHE 0.029 0.001 PHE C 172 TRP 0.007 0.001 TRP C 64 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 3714) covalent geometry : angle 0.57328 / 0.29 ( 5052) SS BOND : bond 0.00083 / 0.05 ( 4) SS BOND : angle 0.93435 / 0.61 ( 8) hydrogen bonds : bond 0.02634 / 1.76 ( 107) hydrogen bonds : angle 5.84650 / 4.00 ( 264) link_NAG-ASN : bond 0.00271 / 0.15 ( 6) link_NAG-ASN : angle 1.94039 / 1.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8452 (mt-10) REVERT: A 448 ASN cc_start: 0.6349 (OUTLIER) cc_final: 0.5680 (m-40) REVERT: A 496 SER cc_start: 0.8464 (m) cc_final: 0.7991 (t) REVERT: C 52 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8821 (tm-30) REVERT: C 186 PHE cc_start: 0.6769 (p90) cc_final: 0.6371 (p90) REVERT: C 214 ASP cc_start: 0.8327 (m-30) cc_final: 0.7996 (m-30) REVERT: C 217 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8601 (mm-40) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.5863 time to fit residues: 38.6666 Evaluate side-chains 61 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 217 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.100475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073214 restraints weight = 6834.300| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.39 r_work: 0.2911 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3724 Z= 0.120 Angle : 0.588 9.361 5078 Z= 0.296 Chirality : 0.047 0.201 561 Planarity : 0.004 0.038 639 Dihedral : 6.049 56.878 601 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.05 % Allowed : 25.83 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.40), residues: 422 helix: -2.71 (0.84), residues: 21 sheet: 0.21 (0.46), residues: 120 loop : -0.79 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 213 TYR 0.011 0.001 TYR A 489 PHE 0.010 0.001 PHE C 133 TRP 0.006 0.001 TRP C 64 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3714) covalent geometry : angle 0.57766 / 0.29 ( 5052) SS BOND : bond 0.00151 / 0.10 ( 4) SS BOND : angle 0.92337 / 0.61 ( 8) hydrogen bonds : bond 0.02591 / 1.73 ( 107) hydrogen bonds : angle 5.81561 / 3.97 ( 264) link_NAG-ASN : bond 0.00289 / 0.16 ( 6) link_NAG-ASN : angle 1.90382 / 1.10 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8478 (mt-10) REVERT: A 448 ASN cc_start: 0.6230 (OUTLIER) cc_final: 0.5579 (m-40) REVERT: A 496 SER cc_start: 0.8463 (m) cc_final: 0.8007 (t) REVERT: C 52 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8830 (tm-30) REVERT: C 186 PHE cc_start: 0.6878 (p90) cc_final: 0.6363 (p90) REVERT: C 214 ASP cc_start: 0.8244 (m-30) cc_final: 0.7936 (m-30) REVERT: C 217 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8609 (mm-40) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.6804 time to fit residues: 42.7309 Evaluate side-chains 61 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 217 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 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 = 0.3498 r_free = 0.3498 target = 0.099453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.072281 restraints weight = 6676.835| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.36 r_work: 0.2889 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3724 Z= 0.148 Angle : 0.593 9.304 5078 Z= 0.299 Chirality : 0.047 0.205 561 Planarity : 0.004 0.040 639 Dihedral : 6.099 56.991 601 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.05 % Allowed : 26.09 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.39), residues: 422 helix: -2.55 (0.87), residues: 20 sheet: 0.17 (0.45), residues: 122 loop : -0.85 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 213 TYR 0.011 0.001 TYR A 489 PHE 0.033 0.001 PHE C 172 TRP 0.007 0.001 TRP C 64 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 3714) covalent geometry : angle 0.58182 / 0.30 ( 5052) SS BOND : bond 0.00172 / 0.11 ( 4) SS BOND : angle 0.97081 / 0.64 ( 8) hydrogen bonds : bond 0.02708 / 1.80 ( 107) hydrogen bonds : angle 5.82534 / 4.00 ( 264) link_NAG-ASN : bond 0.00231 / 0.13 ( 6) link_NAG-ASN : angle 1.93612 / 1.12 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1526.48 seconds wall clock time: 26 minutes 44.89 seconds (1604.89 seconds total)