Starting phenix.real_space_refine on Wed Jul 1 21:16:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mji_23874/07_2026/7mji_23874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mji_23874/07_2026/7mji_23874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2026/7mji_23874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2026/7mji_23874.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2026/7mji_23874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2026/7mji_23874.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2026/7mji_23874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2026/7mji_23874.cif" } resolution = 2.81 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= 0.024 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 14 5.16 5 C 1597 2.51 5 N 425 2.21 5 O 486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2522 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" 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: 0.86, per 1000 atoms: 0.34 Number of scatterers: 2522 At special positions: 0 Unit cell: (84, 59, 79, 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 14 16.00 O 486 8.00 N 425 7.00 C 1597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 116 " distance=2.02 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 B1301 " - " ASN B 343 " Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 95.1 milliseconds 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 582 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 16.6% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.648A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.555A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.614A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 removed outlier: 4.400A pdb=" N ASP E 52 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR E 53 " --> pdb=" O PHE E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 49 through 53' Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 107 through 111 removed outlier: 3.511A pdb=" N THR E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.835A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.835A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 24 through 28 removed outlier: 3.644A pdb=" N LEU E 99 " --> pdb=" O CYS E 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.611A pdb=" N MET E 55 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG E 71 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 57 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.140A pdb=" N VAL E 134 " --> pdb=" O ARG E 118 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 210 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: 0.28 Time building geometry restraints manager: 0.29 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: 813 1.34 - 1.46: 685 1.46 - 1.58: 1070 1.58 - 1.71: 0 1.71 - 1.83: 18 Bond restraints: 2586 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" CG LEU E 41 " pdb=" CD1 LEU E 41 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.52e+00 bond pdb=" C TYR B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.340 1.266 0.074 5.87e-02 2.90e+02 1.58e+00 bond pdb=" CG1 ILE E 69 " pdb=" CD1 ILE E 69 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 ... (remaining 2581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 3354 1.81 - 3.63: 139 3.63 - 5.44: 18 5.44 - 7.25: 3 7.25 - 9.06: 1 Bond angle restraints: 3515 Sorted by residual: angle pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 112.60 115.23 -2.63 1.00e+00 1.00e+00 6.90e+00 angle pdb=" CA LEU E 84 " pdb=" CB LEU E 84 " pdb=" CG LEU E 84 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 angle pdb=" C LYS E 96 " pdb=" N ASN E 97 " pdb=" CA ASN E 97 " ideal model delta sigma weight residual 122.36 125.96 -3.60 1.42e+00 4.96e-01 6.41e+00 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.93 126.73 -3.80 1.51e+00 4.39e-01 6.33e+00 angle pdb=" CB ARG E 59 " pdb=" CG ARG E 59 " pdb=" CD ARG E 59 " ideal model delta sigma weight residual 111.30 116.91 -5.61 2.30e+00 1.89e-01 5.95e+00 ... (remaining 3510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 1376 15.39 - 30.77: 108 30.77 - 46.15: 18 46.15 - 61.54: 6 61.54 - 76.92: 5 Dihedral angle restraints: 1513 sinusoidal: 589 harmonic: 924 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" N GLY B 404 " pdb=" CA GLY B 404 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE B 515 " pdb=" C PHE B 515 " pdb=" N GLU B 516 " pdb=" CA GLU B 516 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 175 0.032 - 0.063: 114 0.063 - 0.095: 52 0.095 - 0.127: 26 0.127 - 0.158: 7 Chirality restraints: 374 Sorted by residual: chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 371 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 103 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C MET E 103 " 0.040 2.00e-02 2.50e+03 pdb=" O MET E 103 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN E 104 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 43 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C CYS E 43 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS E 43 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 44 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 521 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.030 5.00e-02 4.00e+02 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 917 2.87 - 3.38: 2025 3.38 - 3.89: 4248 3.89 - 4.39: 4808 4.39 - 4.90: 8495 Nonbonded interactions: 20493 Sorted by model distance: nonbonded pdb=" OG SER B 366 " pdb=" OD1 ASN B 388 " model vdw 2.367 3.040 nonbonded pdb=" NE ARG E 71 " pdb=" OD2 ASP E 119 " model vdw 2.373 3.120 nonbonded pdb=" NE2 GLN E 60 " pdb=" O LYS E 64 " model vdw 2.446 3.120 nonbonded pdb=" OH TYR B 489 " pdb=" NH2 ARG E 124 " model vdw 2.474 3.120 nonbonded pdb=" NE ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.492 3.120 ... (remaining 20488 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: 4.450 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.440 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.006 0.074 2592 Z= 0.258 Angle : 0.818 9.063 3528 Z= 0.430 Chirality : 0.053 0.158 374 Planarity : 0.008 0.070 458 Dihedral : 12.457 76.924 916 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.83 (0.44), residues: 316 helix: -4.87 (0.21), residues: 27 sheet: 0.26 (0.55), residues: 93 loop : -0.23 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 357 TYR 0.021 0.002 TYR B 495 PHE 0.017 0.002 PHE B 377 TRP 0.016 0.002 TRP E 68 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 ( 2586) covalent geometry : angle 0.80814 / 0.43 ( 3515) SS BOND : bond 0.00448 / 0.31 ( 5) SS BOND : angle 1.73843 / 1.12 ( 10) hydrogen bonds : bond 0.14570 / 9.63 ( 78) hydrogen bonds : angle 9.73884 / 6.75 ( 210) link_NAG-ASN : bond 0.00920 / 0.48 ( 1) link_NAG-ASN : angle 3.50596 / 1.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.097 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.4676 time to fit residues: 35.4788 Evaluate side-chains 63 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.0010 chunk 29 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 ASN B 388 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.084491 restraints weight = 4337.365| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.68 r_work: 0.3089 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2592 Z= 0.148 Angle : 0.528 4.287 3528 Z= 0.273 Chirality : 0.043 0.130 374 Planarity : 0.004 0.030 458 Dihedral : 4.430 17.523 359 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.31 % Allowed : 11.40 % Favored : 85.29 % 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: -0.19 (0.47), residues: 316 helix: -4.13 (0.44), residues: 28 sheet: 0.57 (0.54), residues: 99 loop : 0.27 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.013 0.001 TYR B 365 PHE 0.010 0.001 PHE B 377 TRP 0.009 0.001 TRP E 57 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 2586) covalent geometry : angle 0.52342 / 0.27 ( 3515) SS BOND : bond 0.00463 / 0.25 ( 5) SS BOND : angle 1.22520 / 0.78 ( 10) hydrogen bonds : bond 0.04006 / 2.37 ( 78) hydrogen bonds : angle 7.33063 / 5.00 ( 210) link_NAG-ASN : bond 0.00469 / 0.25 ( 1) link_NAG-ASN : angle 1.56573 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.117 Fit side-chains REVERT: B 360 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8518 (t0) REVERT: B 394 ASN cc_start: 0.7351 (m-40) cc_final: 0.7083 (p0) REVERT: E 42 SER cc_start: 0.8626 (m) cc_final: 0.8386 (p) REVERT: E 77 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7951 (ptp90) outliers start: 9 outliers final: 4 residues processed: 76 average time/residue: 0.4119 time to fit residues: 32.1523 Evaluate side-chains 75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082740 restraints weight = 4438.702| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.69 r_work: 0.3057 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2592 Z= 0.182 Angle : 0.531 4.373 3528 Z= 0.273 Chirality : 0.044 0.140 374 Planarity : 0.003 0.029 458 Dihedral : 4.312 17.257 359 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.84 % Allowed : 15.81 % Favored : 82.35 % 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: -0.05 (0.47), residues: 316 helix: -3.46 (0.72), residues: 28 sheet: 0.58 (0.56), residues: 89 loop : 0.32 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 92 TYR 0.013 0.001 TYR B 495 PHE 0.007 0.001 PHE B 377 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 2586) covalent geometry : angle 0.52344 / 0.27 ( 3515) SS BOND : bond 0.00280 / 0.17 ( 5) SS BOND : angle 1.65097 / 0.98 ( 10) hydrogen bonds : bond 0.03565 / 2.07 ( 78) hydrogen bonds : angle 7.05141 / 4.79 ( 210) link_NAG-ASN : bond 0.00401 / 0.21 ( 1) link_NAG-ASN : angle 1.05759 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.130 Fit side-chains REVERT: E 42 SER cc_start: 0.8524 (m) cc_final: 0.8247 (p) outliers start: 5 outliers final: 5 residues processed: 76 average time/residue: 0.4115 time to fit residues: 32.2205 Evaluate side-chains 75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 12 optimal weight: 0.0470 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN B 409 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.093991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082810 restraints weight = 4395.910| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.66 r_work: 0.3059 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2592 Z= 0.163 Angle : 0.516 5.014 3528 Z= 0.267 Chirality : 0.044 0.153 374 Planarity : 0.003 0.028 458 Dihedral : 4.211 16.064 359 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.31 % Allowed : 15.81 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.47), residues: 316 helix: -3.17 (0.85), residues: 28 sheet: 0.52 (0.56), residues: 89 loop : 0.44 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 357 TYR 0.012 0.001 TYR B 495 PHE 0.006 0.001 PHE B 377 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 2586) covalent geometry : angle 0.50976 / 0.26 ( 3515) SS BOND : bond 0.00356 / 0.19 ( 5) SS BOND : angle 1.42082 / 0.83 ( 10) hydrogen bonds : bond 0.03110 / 1.79 ( 78) hydrogen bonds : angle 6.88879 / 4.68 ( 210) link_NAG-ASN : bond 0.00333 / 0.18 ( 1) link_NAG-ASN : angle 1.18084 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.062 Fit side-chains REVERT: E 42 SER cc_start: 0.8485 (m) cc_final: 0.8184 (p) REVERT: E 77 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8086 (ptp90) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.3841 time to fit residues: 29.0656 Evaluate side-chains 75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 14 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.094612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083584 restraints weight = 4436.429| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.65 r_work: 0.3071 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2592 Z= 0.137 Angle : 0.521 5.199 3528 Z= 0.267 Chirality : 0.043 0.146 374 Planarity : 0.003 0.026 458 Dihedral : 4.124 16.071 359 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.21 % Allowed : 16.91 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.47), residues: 316 helix: -3.29 (1.08), residues: 21 sheet: 0.13 (0.56), residues: 84 loop : 0.45 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.010 0.001 TYR B 495 PHE 0.006 0.001 PHE B 392 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 2586) covalent geometry : angle 0.51696 / 0.27 ( 3515) SS BOND : bond 0.00459 / 0.23 ( 5) SS BOND : angle 1.24610 / 0.73 ( 10) hydrogen bonds : bond 0.03113 / 1.80 ( 78) hydrogen bonds : angle 6.70444 / 4.57 ( 210) link_NAG-ASN : bond 0.00318 / 0.17 ( 1) link_NAG-ASN : angle 1.21417 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.107 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 0.3474 time to fit residues: 26.7576 Evaluate side-chains 76 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.094027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083081 restraints weight = 4450.621| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.62 r_work: 0.3061 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2592 Z= 0.155 Angle : 0.524 5.926 3528 Z= 0.267 Chirality : 0.043 0.149 374 Planarity : 0.003 0.026 458 Dihedral : 4.109 16.193 359 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.31 % Allowed : 17.28 % Favored : 79.41 % 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: 0.03 (0.47), residues: 316 helix: -3.21 (1.08), residues: 21 sheet: 0.12 (0.56), residues: 84 loop : 0.47 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 346 TYR 0.010 0.001 TYR B 495 PHE 0.007 0.001 PHE B 515 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 2586) covalent geometry : angle 0.51885 / 0.26 ( 3515) SS BOND : bond 0.00394 / 0.21 ( 5) SS BOND : angle 1.27862 / 0.73 ( 10) hydrogen bonds : bond 0.02973 / 1.70 ( 78) hydrogen bonds : angle 6.63468 / 4.52 ( 210) link_NAG-ASN : bond 0.00300 / 0.16 ( 1) link_NAG-ASN : angle 1.24305 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.098 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.4614 time to fit residues: 35.1228 Evaluate side-chains 76 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.093999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082980 restraints weight = 4274.498| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.61 r_work: 0.3062 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2592 Z= 0.157 Angle : 0.530 6.321 3528 Z= 0.270 Chirality : 0.044 0.151 374 Planarity : 0.003 0.026 458 Dihedral : 4.116 16.012 359 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.04 % Allowed : 16.18 % Favored : 79.78 % 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: -0.02 (0.47), residues: 316 helix: -3.19 (1.07), residues: 21 sheet: 0.06 (0.56), residues: 84 loop : 0.44 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.010 0.001 TYR B 495 PHE 0.010 0.001 PHE B 392 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 2586) covalent geometry : angle 0.52522 / 0.27 ( 3515) SS BOND : bond 0.00334 / 0.18 ( 5) SS BOND : angle 1.34868 / 0.76 ( 10) hydrogen bonds : bond 0.02984 / 1.71 ( 78) hydrogen bonds : angle 6.65161 / 4.55 ( 210) link_NAG-ASN : bond 0.00297 / 0.16 ( 1) link_NAG-ASN : angle 1.24965 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.100 Fit side-chains REVERT: B 360 ASN cc_start: 0.8962 (t0) cc_final: 0.8518 (t0) REVERT: E 119 ASP cc_start: 0.8588 (m-30) cc_final: 0.8318 (m-30) REVERT: E 132 MET cc_start: 0.8702 (mmt) cc_final: 0.7803 (mmt) outliers start: 11 outliers final: 10 residues processed: 77 average time/residue: 0.3836 time to fit residues: 30.4593 Evaluate side-chains 80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 144 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 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 = 0.3328 r_free = 0.3328 target = 0.094312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.083173 restraints weight = 4404.698| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.70 r_work: 0.3051 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2592 Z= 0.162 Angle : 0.530 6.810 3528 Z= 0.268 Chirality : 0.044 0.154 374 Planarity : 0.003 0.027 458 Dihedral : 4.143 16.071 359 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.78 % Allowed : 15.44 % Favored : 79.78 % 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: -0.03 (0.47), residues: 316 helix: -3.12 (1.09), residues: 21 sheet: 0.09 (0.56), residues: 84 loop : 0.39 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.015 0.001 TYR B 365 PHE 0.010 0.001 PHE B 392 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 2586) covalent geometry : angle 0.52465 / 0.27 ( 3515) SS BOND : bond 0.00370 / 0.20 ( 5) SS BOND : angle 1.35358 / 0.75 ( 10) hydrogen bonds : bond 0.02896 / 1.66 ( 78) hydrogen bonds : angle 6.66751 / 4.57 ( 210) link_NAG-ASN : bond 0.00264 / 0.14 ( 1) link_NAG-ASN : angle 1.26144 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.100 Fit side-chains REVERT: B 360 ASN cc_start: 0.9010 (t0) cc_final: 0.8563 (t0) REVERT: E 119 ASP cc_start: 0.8606 (m-30) cc_final: 0.8301 (m-30) REVERT: E 132 MET cc_start: 0.8727 (mmt) cc_final: 0.7833 (mmt) outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 0.3914 time to fit residues: 29.8519 Evaluate side-chains 73 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.095299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084060 restraints weight = 4410.113| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.67 r_work: 0.3080 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2592 Z= 0.120 Angle : 0.537 7.207 3528 Z= 0.274 Chirality : 0.044 0.152 374 Planarity : 0.003 0.029 458 Dihedral : 4.062 15.575 359 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.57 % Allowed : 18.75 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.47), residues: 316 helix: -3.16 (1.06), residues: 21 sheet: 0.15 (0.57), residues: 82 loop : 0.37 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.013 0.001 TYR B 365 PHE 0.008 0.001 PHE B 392 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 2586) covalent geometry : angle 0.53155 / 0.27 ( 3515) SS BOND : bond 0.00390 / 0.20 ( 5) SS BOND : angle 1.37880 / 0.79 ( 10) hydrogen bonds : bond 0.03016 / 1.75 ( 78) hydrogen bonds : angle 6.54597 / 4.54 ( 210) link_NAG-ASN : bond 0.00286 / 0.15 ( 1) link_NAG-ASN : angle 1.24128 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.100 Fit side-chains REVERT: B 360 ASN cc_start: 0.9008 (t0) cc_final: 0.8569 (t0) REVERT: B 424 LYS cc_start: 0.9028 (tptp) cc_final: 0.8630 (tppp) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.4391 time to fit residues: 32.1281 Evaluate side-chains 69 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 20 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.094789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083911 restraints weight = 4394.899| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.56 r_work: 0.3080 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2592 Z= 0.134 Angle : 0.545 7.397 3528 Z= 0.277 Chirality : 0.044 0.148 374 Planarity : 0.003 0.030 458 Dihedral : 4.065 15.776 359 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.84 % Allowed : 19.85 % Favored : 78.31 % 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: 0.06 (0.47), residues: 316 helix: -3.11 (1.07), residues: 21 sheet: 0.21 (0.58), residues: 82 loop : 0.44 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.016 0.001 TYR B 365 PHE 0.007 0.001 PHE B 392 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 2586) covalent geometry : angle 0.53919 / 0.27 ( 3515) SS BOND : bond 0.00395 / 0.20 ( 5) SS BOND : angle 1.47586 / 0.82 ( 10) hydrogen bonds : bond 0.02964 / 1.71 ( 78) hydrogen bonds : angle 6.54078 / 4.51 ( 210) link_NAG-ASN : bond 0.00279 / 0.15 ( 1) link_NAG-ASN : angle 1.26492 / 0.72 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.099 Fit side-chains REVERT: B 360 ASN cc_start: 0.9026 (t0) cc_final: 0.8575 (t0) REVERT: B 424 LYS cc_start: 0.9031 (tptp) cc_final: 0.8630 (tppp) REVERT: E 119 ASP cc_start: 0.8548 (m-30) cc_final: 0.8230 (m-30) REVERT: E 132 MET cc_start: 0.8735 (mmt) cc_final: 0.7854 (mmt) outliers start: 5 outliers final: 5 residues processed: 70 average time/residue: 0.4403 time to fit residues: 31.7166 Evaluate side-chains 71 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.091695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080809 restraints weight = 4383.501| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.58 r_work: 0.3007 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 2592 Z= 0.230 Angle : 0.606 7.656 3528 Z= 0.308 Chirality : 0.046 0.162 374 Planarity : 0.003 0.028 458 Dihedral : 4.384 16.520 359 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.31 % Allowed : 20.59 % Favored : 76.10 % 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: -0.13 (0.47), residues: 316 helix: -2.74 (0.94), residues: 28 sheet: -0.05 (0.58), residues: 82 loop : 0.44 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.019 0.001 TYR B 365 PHE 0.009 0.001 PHE B 515 TRP 0.009 0.001 TRP E 68 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 ( 2586) covalent geometry : angle 0.59927 / 0.31 ( 3515) SS BOND : bond 0.00494 / 0.26 ( 5) SS BOND : angle 1.65095 / 0.94 ( 10) hydrogen bonds : bond 0.03222 / 1.85 ( 78) hydrogen bonds : angle 6.81018 / 4.70 ( 210) link_NAG-ASN : bond 0.00222 / 0.12 ( 1) link_NAG-ASN : angle 1.33478 / 0.70 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.23 seconds wall clock time: 23 minutes 14.75 seconds (1394.75 seconds total)