Starting phenix.real_space_refine on Wed Jul 23 09:08:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mji_23874/07_2025/7mji_23874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mji_23874/07_2025/7mji_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_2025/7mji_23874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2025/7mji_23874.map" model { file = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2025/7mji_23874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mji_23874/07_2025/7mji_23874.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.13, per 1000 atoms: 1.64 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: 0.59 Conformation dependent library (CDL) restraints added in 311.6 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: 0.37 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: 0.65 Time building geometry restraints manager: 0.73 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: 1393 15.39 - 30.77: 110 30.77 - 46.15: 20 46.15 - 61.54: 6 61.54 - 76.92: 5 Dihedral angle restraints: 1534 sinusoidal: 610 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 1531 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: 2.910 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 12.491 76.924 937 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP E 68 HIS 0.002 0.001 HIS B 519 PHE 0.017 0.002 PHE B 377 TYR 0.021 0.002 TYR B 495 ARG 0.017 0.002 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00920 ( 1) link_NAG-ASN : angle 3.50596 ( 3) hydrogen bonds : bond 0.14570 ( 78) hydrogen bonds : angle 9.73884 ( 210) SS BOND : bond 0.00448 ( 5) SS BOND : angle 1.73843 ( 10) covalent geometry : bond 0.00613 ( 2586) covalent geometry : angle 0.80814 ( 3515) *********************** 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 : 0.271 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 1.1288 time to fit residues: 85.8302 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 : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.085116 restraints weight = 4346.347| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.66 r_work: 0.3100 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1820 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= 0.132 Angle : 0.518 4.386 3528 Z= 0.269 Chirality : 0.042 0.131 374 Planarity : 0.004 0.030 458 Dihedral : 5.144 38.342 380 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.31 % Allowed : 11.76 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.47), residues: 316 helix: -4.14 (0.44), residues: 28 sheet: 0.58 (0.54), residues: 99 loop : 0.27 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.001 0.000 HIS B 519 PHE 0.009 0.001 PHE B 377 TYR 0.013 0.001 TYR B 365 ARG 0.006 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 1) link_NAG-ASN : angle 2.17882 ( 3) hydrogen bonds : bond 0.03992 ( 78) hydrogen bonds : angle 7.34017 ( 210) SS BOND : bond 0.00239 ( 5) SS BOND : angle 1.26858 ( 10) covalent geometry : bond 0.00303 ( 2586) covalent geometry : angle 0.51063 ( 3515) *********************** 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 82 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.294 Fit side-chains REVERT: B 360 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8498 (t0) REVERT: B 394 ASN cc_start: 0.7347 (m-40) cc_final: 0.7060 (p0) REVERT: E 42 SER cc_start: 0.8664 (m) cc_final: 0.8384 (p) outliers start: 9 outliers final: 4 residues processed: 74 average time/residue: 0.9688 time to fit residues: 73.7270 Evaluate side-chains 72 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ASN 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 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B 370 ASN B 388 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.095348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084150 restraints weight = 4169.643| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.51 r_work: 0.3051 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2592 Z= 0.192 Angle : 0.534 4.437 3528 Z= 0.277 Chirality : 0.043 0.131 374 Planarity : 0.004 0.028 458 Dihedral : 5.401 43.623 380 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.04 % Allowed : 13.97 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.47), residues: 316 helix: -3.51 (0.71), residues: 28 sheet: 0.59 (0.56), residues: 89 loop : 0.30 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.001 0.001 HIS B 519 PHE 0.008 0.001 PHE B 377 TYR 0.014 0.001 TYR B 495 ARG 0.006 0.001 ARG E 92 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 1) link_NAG-ASN : angle 1.80872 ( 3) hydrogen bonds : bond 0.03595 ( 78) hydrogen bonds : angle 7.07180 ( 210) SS BOND : bond 0.00288 ( 5) SS BOND : angle 1.54397 ( 10) covalent geometry : bond 0.00438 ( 2586) covalent geometry : angle 0.52587 ( 3515) *********************** 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 85 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.297 Fit side-chains REVERT: E 42 SER cc_start: 0.8574 (m) cc_final: 0.8301 (p) REVERT: E 77 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8114 (ptp90) outliers start: 11 outliers final: 5 residues processed: 78 average time/residue: 1.0357 time to fit residues: 82.9310 Evaluate side-chains 77 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3310 r_free = 0.3310 target = 0.092598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081371 restraints weight = 4412.054| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.66 r_work: 0.3032 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 2592 Z= 0.221 Angle : 0.560 5.229 3528 Z= 0.290 Chirality : 0.045 0.155 374 Planarity : 0.004 0.027 458 Dihedral : 5.642 46.199 380 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.04 % Allowed : 13.24 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.46), residues: 316 helix: -3.11 (0.88), residues: 28 sheet: -0.08 (0.56), residues: 82 loop : 0.40 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 68 HIS 0.002 0.001 HIS B 519 PHE 0.014 0.001 PHE B 392 TYR 0.014 0.001 TYR B 495 ARG 0.006 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 1) link_NAG-ASN : angle 2.02487 ( 3) hydrogen bonds : bond 0.03349 ( 78) hydrogen bonds : angle 7.04079 ( 210) SS BOND : bond 0.00201 ( 5) SS BOND : angle 1.55691 ( 10) covalent geometry : bond 0.00510 ( 2586) covalent geometry : angle 0.55153 ( 3515) *********************** 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 83 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.272 Fit side-chains REVERT: E 42 SER cc_start: 0.8523 (m) cc_final: 0.8199 (p) REVERT: E 77 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8085 (ptp90) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 1.0061 time to fit residues: 76.7553 Evaluate side-chains 77 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.093654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082471 restraints weight = 4403.550| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.66 r_work: 0.3053 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2592 Z= 0.161 Angle : 0.527 5.343 3528 Z= 0.273 Chirality : 0.044 0.146 374 Planarity : 0.003 0.029 458 Dihedral : 5.406 43.561 380 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.68 % Allowed : 15.81 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.47), residues: 316 helix: -2.86 (0.93), residues: 28 sheet: -0.12 (0.54), residues: 84 loop : 0.50 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.010 0.001 PHE B 392 TYR 0.011 0.001 TYR B 495 ARG 0.006 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 1) link_NAG-ASN : angle 1.97883 ( 3) hydrogen bonds : bond 0.03148 ( 78) hydrogen bonds : angle 6.82091 ( 210) SS BOND : bond 0.00389 ( 5) SS BOND : angle 1.29130 ( 10) covalent geometry : bond 0.00371 ( 2586) covalent geometry : angle 0.52047 ( 3515) *********************** 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 81 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.270 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 1.0336 time to fit residues: 77.4770 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 : 0.380 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081273 restraints weight = 4441.020| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.64 r_work: 0.3032 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 2592 Z= 0.214 Angle : 0.551 6.221 3528 Z= 0.283 Chirality : 0.044 0.137 374 Planarity : 0.003 0.029 458 Dihedral : 5.643 46.475 380 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.94 % Allowed : 16.91 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.47), residues: 316 helix: -2.78 (0.94), residues: 28 sheet: -0.21 (0.56), residues: 82 loop : 0.44 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 68 HIS 0.002 0.001 HIS B 519 PHE 0.008 0.001 PHE B 392 TYR 0.013 0.001 TYR B 365 ARG 0.006 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 2.10213 ( 3) hydrogen bonds : bond 0.03099 ( 78) hydrogen bonds : angle 6.87124 ( 210) SS BOND : bond 0.00426 ( 5) SS BOND : angle 1.39645 ( 10) covalent geometry : bond 0.00492 ( 2586) covalent geometry : angle 0.54360 ( 3515) *********************** 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 75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.306 Fit side-chains REVERT: B 360 ASN cc_start: 0.8970 (t0) cc_final: 0.8646 (t0) REVERT: E 119 ASP cc_start: 0.8654 (m-30) cc_final: 0.8375 (m-30) REVERT: E 132 MET cc_start: 0.8717 (mmt) cc_final: 0.7823 (mmt) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 1.0025 time to fit residues: 74.1873 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 : 0.288 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.082414 restraints weight = 4504.895| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.70 r_work: 0.3048 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2592 Z= 0.146 Angle : 0.518 6.432 3528 Z= 0.265 Chirality : 0.043 0.131 374 Planarity : 0.003 0.029 458 Dihedral : 5.340 42.805 380 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.57 % Allowed : 18.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.47), residues: 316 helix: -2.80 (0.92), residues: 28 sheet: -0.17 (0.55), residues: 84 loop : 0.52 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.007 0.001 PHE B 515 TYR 0.011 0.001 TYR B 365 ARG 0.006 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 1) link_NAG-ASN : angle 2.05822 ( 3) hydrogen bonds : bond 0.02845 ( 78) hydrogen bonds : angle 6.73717 ( 210) SS BOND : bond 0.00320 ( 5) SS BOND : angle 1.30706 ( 10) covalent geometry : bond 0.00339 ( 2586) covalent geometry : angle 0.51048 ( 3515) *********************** 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 75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.301 Fit side-chains REVERT: B 360 ASN cc_start: 0.8986 (t0) cc_final: 0.8648 (t0) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.9603 time to fit residues: 70.1327 Evaluate side-chains 72 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 91 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.092472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081686 restraints weight = 4384.201| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.57 r_work: 0.3020 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2592 Z= 0.170 Angle : 0.543 6.932 3528 Z= 0.278 Chirality : 0.044 0.132 374 Planarity : 0.003 0.028 458 Dihedral : 5.435 44.070 380 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.21 % Allowed : 18.75 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.47), residues: 316 helix: -2.73 (0.96), residues: 27 sheet: -0.14 (0.57), residues: 82 loop : 0.44 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 68 HIS 0.002 0.001 HIS B 519 PHE 0.006 0.001 PHE B 392 TYR 0.016 0.001 TYR B 365 ARG 0.007 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 2.08895 ( 3) hydrogen bonds : bond 0.03008 ( 78) hydrogen bonds : angle 6.74913 ( 210) SS BOND : bond 0.00370 ( 5) SS BOND : angle 1.42109 ( 10) covalent geometry : bond 0.00392 ( 2586) covalent geometry : angle 0.53520 ( 3515) *********************** 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 70 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.293 Fit side-chains REVERT: B 360 ASN cc_start: 0.9003 (t0) cc_final: 0.8663 (t0) REVERT: E 85 LYS cc_start: 0.7677 (tttm) cc_final: 0.7295 (mtpm) REVERT: E 119 ASP cc_start: 0.8618 (m-30) cc_final: 0.8343 (m-30) REVERT: E 132 MET cc_start: 0.8704 (mmt) cc_final: 0.7835 (mmt) outliers start: 6 outliers final: 6 residues processed: 67 average time/residue: 1.0683 time to fit residues: 73.4758 Evaluate side-chains 70 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 87 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.083053 restraints weight = 4330.999| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.56 r_work: 0.3047 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3101 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= 0.128 Angle : 0.531 6.898 3528 Z= 0.273 Chirality : 0.043 0.131 374 Planarity : 0.003 0.029 458 Dihedral : 5.229 41.144 380 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.57 % Allowed : 18.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.48), residues: 316 helix: -2.74 (0.96), residues: 27 sheet: 0.01 (0.56), residues: 84 loop : 0.51 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.006 0.001 PHE B 392 TYR 0.014 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 1) link_NAG-ASN : angle 2.08025 ( 3) hydrogen bonds : bond 0.02960 ( 78) hydrogen bonds : angle 6.74781 ( 210) SS BOND : bond 0.00415 ( 5) SS BOND : angle 1.42513 ( 10) covalent geometry : bond 0.00297 ( 2586) covalent geometry : angle 0.52346 ( 3515) *********************** 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 70 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.271 Fit side-chains REVERT: B 360 ASN cc_start: 0.8995 (t0) cc_final: 0.8641 (t0) REVERT: B 424 LYS cc_start: 0.8999 (tptp) cc_final: 0.8583 (tppp) REVERT: E 27 GLU cc_start: 0.8594 (pm20) cc_final: 0.8366 (pm20) outliers start: 7 outliers final: 6 residues processed: 67 average time/residue: 1.0718 time to fit residues: 73.6822 Evaluate side-chains 67 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082963 restraints weight = 4326.217| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.56 r_work: 0.3042 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3154 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= 0.137 Angle : 0.537 7.405 3528 Z= 0.274 Chirality : 0.043 0.131 374 Planarity : 0.003 0.029 458 Dihedral : 5.221 41.555 380 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.57 % Allowed : 18.38 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.47), residues: 316 helix: -3.10 (1.09), residues: 21 sheet: 0.17 (0.57), residues: 82 loop : 0.37 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.009 0.001 PHE B 515 TYR 0.016 0.001 TYR B 365 ARG 0.007 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 1) link_NAG-ASN : angle 2.12208 ( 3) hydrogen bonds : bond 0.02912 ( 78) hydrogen bonds : angle 6.71045 ( 210) SS BOND : bond 0.00415 ( 5) SS BOND : angle 1.45528 ( 10) covalent geometry : bond 0.00319 ( 2586) covalent geometry : angle 0.52851 ( 3515) ********************** 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 70 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.270 Fit side-chains REVERT: B 360 ASN cc_start: 0.9015 (t0) cc_final: 0.8658 (t0) REVERT: B 424 LYS cc_start: 0.9013 (tptp) cc_final: 0.8596 (tppp) REVERT: E 119 ASP cc_start: 0.8552 (m-30) cc_final: 0.8281 (m-30) REVERT: E 132 MET cc_start: 0.8698 (mmt) cc_final: 0.7832 (mmt) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.9635 time to fit residues: 66.3497 Evaluate side-chains 66 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083319 restraints weight = 4359.020| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.60 r_work: 0.3049 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3184 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= 0.122 Angle : 0.532 7.314 3528 Z= 0.272 Chirality : 0.043 0.130 374 Planarity : 0.003 0.028 458 Dihedral : 5.122 39.974 380 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.47 % Allowed : 19.49 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.48), residues: 316 helix: -3.09 (1.09), residues: 21 sheet: 0.08 (0.57), residues: 82 loop : 0.40 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.008 0.001 PHE B 392 TYR 0.015 0.001 TYR B 365 ARG 0.007 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 1) link_NAG-ASN : angle 2.11492 ( 3) hydrogen bonds : bond 0.02867 ( 78) hydrogen bonds : angle 6.67333 ( 210) SS BOND : bond 0.00366 ( 5) SS BOND : angle 1.39798 ( 10) covalent geometry : bond 0.00283 ( 2586) covalent geometry : angle 0.52449 ( 3515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2841.46 seconds wall clock time: 49 minutes 2.65 seconds (2942.65 seconds total)