Starting phenix.real_space_refine on Wed Jul 1 22:22:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsc_32753/07_2026/7wsc_32753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsc_32753/07_2026/7wsc_32753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wsc_32753/07_2026/7wsc_32753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsc_32753/07_2026/7wsc_32753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsc_32753/07_2026/7wsc_32753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsc_32753/07_2026/7wsc_32753.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wsc_32753/07_2026/7wsc_32753.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wsc_32753/07_2026/7wsc_32753.cif" } resolution = 3.78 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= 0.019 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 15 5.16 5 C 2156 2.51 5 N 563 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3369 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "H" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 813 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.73, per 1000 atoms: 0.22 Number of scatterers: 3369 At special positions: 0 Unit cell: (63.13, 87.74, 74.9, 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 15 16.00 O 635 8.00 N 563 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.01 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 116.3 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 9.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'R' and resid 338 through 344 Processing helix chain 'R' and resid 364 through 369 removed outlier: 3.593A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 388 removed outlier: 4.117A pdb=" N ASN R 388 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.870A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O VAL H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'L' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.915A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 397 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL R 512 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.861A pdb=" N LEU H 37 " --> pdb=" O MET H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 65 through 70 removed outlier: 6.433A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE H 53 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 144 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.736A pdb=" N THR L 24 " --> pdb=" O ARG L 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.554A pdb=" N ILE L 109 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 183 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: 0.40 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 532 1.26 - 1.40: 979 1.40 - 1.54: 1912 1.54 - 1.68: 17 1.68 - 1.82: 18 Bond restraints: 3458 Sorted by residual: bond pdb=" CA TYR R 380 " pdb=" C TYR R 380 " ideal model delta sigma weight residual 1.524 1.395 0.129 1.35e-02 5.49e+03 9.08e+01 bond pdb=" C PHE R 377 " pdb=" O PHE R 377 " ideal model delta sigma weight residual 1.235 1.116 0.120 1.26e-02 6.30e+03 9.01e+01 bond pdb=" C VAL R 382 " pdb=" O VAL R 382 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.03e-02 9.43e+03 6.47e+01 bond pdb=" CB TYR R 380 " pdb=" CG TYR R 380 " ideal model delta sigma weight residual 1.512 1.341 0.171 2.20e-02 2.07e+03 6.07e+01 bond pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 1.523 1.436 0.088 1.25e-02 6.40e+03 4.91e+01 ... (remaining 3453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 4634 6.03 - 12.06: 48 12.06 - 18.09: 10 18.09 - 24.12: 1 24.12 - 30.15: 2 Bond angle restraints: 4695 Sorted by residual: angle pdb=" N GLY R 482 " pdb=" CA GLY R 482 " pdb=" C GLY R 482 " ideal model delta sigma weight residual 113.18 85.51 27.67 2.37e+00 1.78e-01 1.36e+02 angle pdb=" C PHE R 490 " pdb=" N PRO R 491 " pdb=" CA PRO R 491 " ideal model delta sigma weight residual 119.84 132.96 -13.12 1.25e+00 6.40e-01 1.10e+02 angle pdb=" N PHE R 486 " pdb=" CA PHE R 486 " pdb=" C PHE R 486 " ideal model delta sigma weight residual 111.04 95.20 15.84 1.55e+00 4.16e-01 1.04e+02 angle pdb=" N ALA R 475 " pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 107.98 89.55 18.43 1.88e+00 2.83e-01 9.61e+01 angle pdb=" CA PRO L 37 " pdb=" N PRO L 37 " pdb=" CD PRO L 37 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.23e+01 ... (remaining 4690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1740 15.87 - 31.73: 183 31.73 - 47.60: 57 47.60 - 63.46: 14 63.46 - 79.32: 8 Dihedral angle restraints: 2002 sinusoidal: 785 harmonic: 1217 Sorted by residual: dihedral pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " pdb=" SG CYS R 525 " pdb=" CB CYS R 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.68 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" N CYS R 488 " pdb=" C CYS R 488 " pdb=" CA CYS R 488 " pdb=" CB CYS R 488 " ideal model delta harmonic sigma weight residual 122.80 106.51 16.29 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" CA ARG H 71 " pdb=" C ARG H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 1999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 476 0.158 - 0.317: 11 0.317 - 0.475: 6 0.475 - 0.633: 4 0.633 - 0.791: 2 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA CYS R 379 " pdb=" N CYS R 379 " pdb=" C CYS R 379 " pdb=" CB CYS R 379 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASN R 477 " pdb=" N ASN R 477 " pdb=" C ASN R 477 " pdb=" CB ASN R 477 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.19e+00 ... (remaining 496 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.119 5.00e-02 4.00e+02 1.69e-01 4.60e+01 pdb=" N PRO R 491 " 0.291 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.111 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 368 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C LEU R 368 " 0.111 2.00e-02 2.50e+03 pdb=" O LEU R 368 " -0.042 2.00e-02 2.50e+03 pdb=" N TYR R 369 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 477 " 0.032 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C ASN R 477 " -0.110 2.00e-02 2.50e+03 pdb=" O ASN R 477 " 0.043 2.00e-02 2.50e+03 pdb=" N LYS R 478 " 0.035 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 9 2.26 - 2.92: 1670 2.92 - 3.58: 4936 3.58 - 4.24: 7946 4.24 - 4.90: 13267 Nonbonded interactions: 27828 Sorted by model distance: nonbonded pdb=" O TYR R 473 " pdb=" O CYS R 488 " model vdw 1.600 3.040 nonbonded pdb=" OG1 THR L 33 " pdb=" OE2 GLU L 36 " model vdw 2.071 3.040 nonbonded pdb=" O ASN R 477 " pdb=" ND2 ASN R 477 " model vdw 2.084 3.120 nonbonded pdb=" OG SER H 36 " pdb=" O MET H 102 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP H 73 " pdb=" OG SER H 75 " model vdw 2.118 3.040 ... (remaining 27823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.700 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.171 3465 Z= 0.744 Angle : 1.675 30.153 4711 Z= 0.883 Chirality : 0.101 0.791 499 Planarity : 0.012 0.169 604 Dihedral : 15.388 79.299 1221 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 41.09 Ramachandran Plot: Outliers : 3.62 % Allowed : 14.73 % Favored : 81.64 % Rotamer: Outliers : 4.99 % Allowed : 1.94 % Favored : 93.07 % Cbeta Deviations : 1.31 % Peptide Plane: Cis-proline : 10.00 % 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: -4.09 (0.39), residues: 414 helix: -5.03 (0.30), residues: 12 sheet: -2.57 (0.41), residues: 129 loop : -2.82 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.002 ARG R 493 TYR 0.023 0.002 TYR H 51 PHE 0.056 0.004 PHE R 490 TRP 0.031 0.003 TRP L 59 HIS 0.015 0.005 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.01274 / 0.74 ( 3458) covalent geometry : angle 1.66708 / 0.88 ( 4695) SS BOND : bond 0.01209 / 0.59 ( 5) SS BOND : angle 4.15259 / 3.32 ( 10) hydrogen bonds : bond 0.26234 / 16.92 ( 74) hydrogen bonds : angle 12.54557 / 8.64 ( 183) link_BETA1-4 : bond 0.00848 / 0.45 ( 1) link_BETA1-4 : angle 0.61650 / 0.41 ( 3) link_NAG-ASN : bond 0.00265 / 0.14 ( 1) link_NAG-ASN : angle 0.76176 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.119 Fit side-chains REVERT: R 377 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: R 423 TYR cc_start: 0.7992 (t80) cc_final: 0.7694 (t80) REVERT: R 455 LEU cc_start: 0.7505 (pt) cc_final: 0.7291 (pt) REVERT: R 486 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6241 (t80) REVERT: L 32 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7558 (p) REVERT: L 50 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7214 (tm-30) REVERT: L 111 TYR cc_start: 0.8367 (m-80) cc_final: 0.7828 (m-80) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.0477 time to fit residues: 7.6889 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 474 GLN Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 486 PHE Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain L residue 32 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0060 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.0020 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 474 GLN R 477 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** 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 = 0.3911 r_free = 0.3911 target = 0.145341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120985 restraints weight = 5791.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125231 restraints weight = 3294.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128158 restraints weight = 2237.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.130194 restraints weight = 1690.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131629 restraints weight = 1375.651| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 3465 Z= 0.192 Angle : 0.964 13.390 4711 Z= 0.476 Chirality : 0.055 0.371 499 Planarity : 0.010 0.148 604 Dihedral : 9.867 83.775 500 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.72 % Allowed : 11.59 % Favored : 87.68 % Rotamer: Outliers : 6.09 % Allowed : 14.68 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.59 (0.40), residues: 414 helix: -3.11 (1.13), residues: 12 sheet: -2.50 (0.40), residues: 132 loop : -2.38 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 91 TYR 0.023 0.002 TYR H 51 PHE 0.020 0.002 PHE R 486 TRP 0.017 0.002 TRP L 59 HIS 0.009 0.003 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 3458) covalent geometry : angle 0.95908 / 0.47 ( 4695) SS BOND : bond 0.00336 / 0.22 ( 5) SS BOND : angle 2.24625 / 1.48 ( 10) hydrogen bonds : bond 0.04534 / 2.79 ( 74) hydrogen bonds : angle 8.76167 / 5.87 ( 183) link_BETA1-4 : bond 0.00673 / 0.35 ( 1) link_BETA1-4 : angle 1.00263 / 0.74 ( 3) link_NAG-ASN : bond 0.00271 / 0.14 ( 1) link_NAG-ASN : angle 0.97386 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 374 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.5871 (p90) REVERT: R 377 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: R 423 TYR cc_start: 0.8011 (t80) cc_final: 0.7691 (t80) REVERT: H 134 TYR cc_start: 0.8591 (p90) cc_final: 0.7979 (p90) REVERT: L 26 SER cc_start: 0.6881 (OUTLIER) cc_final: 0.6661 (p) REVERT: L 50 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7534 (tm-30) REVERT: L 111 TYR cc_start: 0.8367 (m-80) cc_final: 0.7637 (m-80) outliers start: 22 outliers final: 15 residues processed: 122 average time/residue: 0.0612 time to fit residues: 9.1330 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 358 ILE Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 488 CYS Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.143101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118793 restraints weight = 5785.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122963 restraints weight = 3312.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125937 restraints weight = 2257.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127957 restraints weight = 1699.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129364 restraints weight = 1378.500| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 3465 Z= 0.186 Angle : 0.860 13.924 4711 Z= 0.433 Chirality : 0.050 0.200 499 Planarity : 0.008 0.139 604 Dihedral : 8.274 58.764 490 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.87 % Favored : 88.41 % Rotamer: Outliers : 5.54 % Allowed : 19.67 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.19 (0.40), residues: 414 helix: -3.09 (1.12), residues: 12 sheet: -2.34 (0.41), residues: 123 loop : -2.05 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 78 TYR 0.021 0.002 TYR R 351 PHE 0.016 0.002 PHE H 48 TRP 0.017 0.002 TRP L 59 HIS 0.004 0.002 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 3458) covalent geometry : angle 0.85662 / 0.43 ( 4695) SS BOND : bond 0.00294 / 0.19 ( 5) SS BOND : angle 1.68057 / 1.04 ( 10) hydrogen bonds : bond 0.03875 / 2.35 ( 74) hydrogen bonds : angle 8.24684 / 5.48 ( 183) link_BETA1-4 : bond 0.00402 / 0.21 ( 1) link_BETA1-4 : angle 1.03105 / 0.82 ( 3) link_NAG-ASN : bond 0.00044 / 0.02 ( 1) link_NAG-ASN : angle 1.19058 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: R 423 TYR cc_start: 0.8018 (t80) cc_final: 0.7673 (t80) REVERT: H 134 TYR cc_start: 0.8702 (p90) cc_final: 0.8154 (p90) REVERT: L 23 MET cc_start: 0.8427 (mmp) cc_final: 0.8067 (mmp) REVERT: L 28 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7155 (tt) REVERT: L 50 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7667 (tm-30) REVERT: L 62 GLN cc_start: 0.8751 (pt0) cc_final: 0.8497 (pt0) REVERT: L 74 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8425 (tt) REVERT: L 111 TYR cc_start: 0.8274 (m-80) cc_final: 0.7660 (m-80) REVERT: L 114 GLN cc_start: 0.9229 (pp30) cc_final: 0.8899 (pt0) outliers start: 20 outliers final: 13 residues processed: 117 average time/residue: 0.0582 time to fit residues: 8.3838 Evaluate side-chains 107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119706 restraints weight = 5711.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123919 restraints weight = 3287.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126804 restraints weight = 2242.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128838 restraints weight = 1705.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130079 restraints weight = 1383.239| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 3465 Z= 0.170 Angle : 0.818 13.522 4711 Z= 0.405 Chirality : 0.048 0.169 499 Planarity : 0.007 0.134 604 Dihedral : 7.654 56.085 485 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.87 % Favored : 88.65 % Rotamer: Outliers : 6.65 % Allowed : 19.94 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.10 (0.41), residues: 414 helix: -2.96 (1.16), residues: 12 sheet: -2.41 (0.41), residues: 130 loop : -1.88 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 91 TYR 0.019 0.002 TYR H 51 PHE 0.013 0.002 PHE H 48 TRP 0.017 0.002 TRP L 59 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 3458) covalent geometry : angle 0.81477 / 0.40 ( 4695) SS BOND : bond 0.00373 / 0.27 ( 5) SS BOND : angle 1.58911 / 0.97 ( 10) hydrogen bonds : bond 0.03699 / 2.28 ( 74) hydrogen bonds : angle 7.73522 / 5.13 ( 183) link_BETA1-4 : bond 0.00335 / 0.18 ( 1) link_BETA1-4 : angle 1.03896 / 0.82 ( 3) link_NAG-ASN : bond 0.00054 / 0.03 ( 1) link_NAG-ASN : angle 1.10184 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: R 423 TYR cc_start: 0.8012 (t80) cc_final: 0.7657 (t80) REVERT: R 489 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6925 (t80) REVERT: R 492 LEU cc_start: 0.8791 (mt) cc_final: 0.8566 (mp) REVERT: L 28 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7259 (tt) REVERT: L 50 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7464 (tm-30) REVERT: L 74 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8501 (tt) REVERT: L 106 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6664 (t0) REVERT: L 111 TYR cc_start: 0.8223 (m-80) cc_final: 0.7760 (m-80) outliers start: 24 outliers final: 16 residues processed: 122 average time/residue: 0.0385 time to fit residues: 5.9077 Evaluate side-chains 116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 106 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.0470 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 450 ASN ** L 25 GLN ** 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 = 0.3940 r_free = 0.3940 target = 0.146317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122288 restraints weight = 5735.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126598 restraints weight = 3282.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129539 restraints weight = 2228.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131542 restraints weight = 1672.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132798 restraints weight = 1355.312| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 3465 Z= 0.145 Angle : 0.804 13.546 4711 Z= 0.395 Chirality : 0.047 0.159 499 Planarity : 0.007 0.129 604 Dihedral : 7.401 52.244 485 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.18 % Favored : 90.34 % Rotamer: Outliers : 6.93 % Allowed : 21.05 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.96 (0.41), residues: 414 helix: -3.36 (0.86), residues: 18 sheet: -2.25 (0.42), residues: 131 loop : -1.73 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 91 TYR 0.016 0.001 TYR L 56 PHE 0.013 0.002 PHE H 133 TRP 0.020 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 ( 3458) covalent geometry : angle 0.80150 / 0.39 ( 4695) SS BOND : bond 0.00248 / 0.14 ( 5) SS BOND : angle 1.53941 / 0.94 ( 10) hydrogen bonds : bond 0.03472 / 2.17 ( 74) hydrogen bonds : angle 7.43580 / 4.92 ( 183) link_BETA1-4 : bond 0.00398 / 0.21 ( 1) link_BETA1-4 : angle 1.03566 / 0.82 ( 3) link_NAG-ASN : bond 0.00057 / 0.03 ( 1) link_NAG-ASN : angle 1.12495 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: R 423 TYR cc_start: 0.7945 (t80) cc_final: 0.7572 (t80) REVERT: R 489 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6977 (t80) REVERT: R 492 LEU cc_start: 0.8698 (mt) cc_final: 0.8432 (mp) REVERT: H 123 TYR cc_start: 0.8640 (p90) cc_final: 0.8322 (p90) REVERT: L 28 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7402 (tt) REVERT: L 50 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7491 (tm-30) REVERT: L 74 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8433 (tt) REVERT: L 111 TYR cc_start: 0.8218 (m-80) cc_final: 0.7659 (m-80) outliers start: 25 outliers final: 15 residues processed: 119 average time/residue: 0.0431 time to fit residues: 6.3836 Evaluate side-chains 121 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117293 restraints weight = 5774.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121284 restraints weight = 3368.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124057 restraints weight = 2321.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125821 restraints weight = 1778.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127335 restraints weight = 1475.370| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 3465 Z= 0.214 Angle : 0.837 13.773 4711 Z= 0.413 Chirality : 0.048 0.164 499 Planarity : 0.007 0.124 604 Dihedral : 7.479 50.793 485 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.84 % Favored : 87.68 % Rotamer: Outliers : 7.76 % Allowed : 21.61 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.99 (0.41), residues: 414 helix: -3.55 (0.79), residues: 18 sheet: -2.25 (0.42), residues: 131 loop : -1.75 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 91 TYR 0.014 0.002 TYR H 78 PHE 0.013 0.002 PHE H 48 TRP 0.021 0.002 TRP L 59 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 ( 3458) covalent geometry : angle 0.83305 / 0.41 ( 4695) SS BOND : bond 0.00327 / 0.20 ( 5) SS BOND : angle 1.79381 / 1.08 ( 10) hydrogen bonds : bond 0.03552 / 2.19 ( 74) hydrogen bonds : angle 7.49220 / 4.96 ( 183) link_BETA1-4 : bond 0.00439 / 0.23 ( 1) link_BETA1-4 : angle 1.18407 / 1.01 ( 3) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 1.13059 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8111 (t80) cc_final: 0.7818 (t80) REVERT: R 489 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.7088 (t80) REVERT: R 492 LEU cc_start: 0.8798 (mt) cc_final: 0.8552 (mp) REVERT: H 95 LYS cc_start: 0.7888 (ptpp) cc_final: 0.7640 (ptpp) REVERT: H 123 TYR cc_start: 0.8608 (p90) cc_final: 0.8310 (p90) REVERT: L 50 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7616 (tm-30) REVERT: L 74 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8586 (tt) REVERT: L 111 TYR cc_start: 0.8208 (m-80) cc_final: 0.7769 (m-80) outliers start: 28 outliers final: 21 residues processed: 116 average time/residue: 0.0372 time to fit residues: 5.3848 Evaluate side-chains 120 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.142213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117996 restraints weight = 5884.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122297 restraints weight = 3308.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125229 restraints weight = 2222.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127255 restraints weight = 1670.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.128385 restraints weight = 1353.671| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 3465 Z= 0.200 Angle : 0.837 13.761 4711 Z= 0.411 Chirality : 0.048 0.149 499 Planarity : 0.007 0.121 604 Dihedral : 7.098 49.351 483 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 7.20 % Allowed : 23.55 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.02 (0.41), residues: 414 helix: -3.51 (0.80), residues: 18 sheet: -2.26 (0.43), residues: 131 loop : -1.78 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 91 TYR 0.011 0.001 TYR H 78 PHE 0.011 0.002 PHE H 48 TRP 0.022 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 ( 3458) covalent geometry : angle 0.83359 / 0.41 ( 4695) SS BOND : bond 0.00276 / 0.14 ( 5) SS BOND : angle 1.75657 / 1.06 ( 10) hydrogen bonds : bond 0.03471 / 2.13 ( 74) hydrogen bonds : angle 7.39806 / 4.89 ( 183) link_BETA1-4 : bond 0.00369 / 0.19 ( 1) link_BETA1-4 : angle 1.08787 / 0.91 ( 3) link_NAG-ASN : bond 0.00041 / 0.02 ( 1) link_NAG-ASN : angle 1.06291 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8140 (t80) cc_final: 0.7906 (t80) REVERT: R 489 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.7149 (t80) REVERT: R 492 LEU cc_start: 0.8790 (mt) cc_final: 0.8572 (mp) REVERT: H 32 GLN cc_start: 0.6286 (mm-40) cc_final: 0.5962 (mm-40) REVERT: H 123 TYR cc_start: 0.8606 (p90) cc_final: 0.8340 (p90) REVERT: L 50 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7641 (tm-30) REVERT: L 74 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8594 (tt) REVERT: L 111 TYR cc_start: 0.8267 (m-80) cc_final: 0.7748 (m-80) outliers start: 26 outliers final: 22 residues processed: 113 average time/residue: 0.0575 time to fit residues: 8.0576 Evaluate side-chains 120 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 17 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.149420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125303 restraints weight = 5800.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129712 restraints weight = 3253.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132764 restraints weight = 2175.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134803 restraints weight = 1618.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136389 restraints weight = 1301.602| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 3465 Z= 0.141 Angle : 0.820 13.462 4711 Z= 0.397 Chirality : 0.046 0.150 499 Planarity : 0.007 0.118 604 Dihedral : 6.816 47.122 483 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.14 % Favored : 89.37 % Rotamer: Outliers : 5.82 % Allowed : 25.76 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.65 (0.42), residues: 414 helix: -3.22 (0.90), residues: 18 sheet: -1.87 (0.44), residues: 135 loop : -1.60 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 91 TYR 0.012 0.001 TYR H 78 PHE 0.009 0.001 PHE H 87 TRP 0.028 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 3458) covalent geometry : angle 0.81723 / 0.40 ( 4695) SS BOND : bond 0.00264 / 0.15 ( 5) SS BOND : angle 1.49862 / 0.92 ( 10) hydrogen bonds : bond 0.03488 / 2.17 ( 74) hydrogen bonds : angle 7.18443 / 4.73 ( 183) link_BETA1-4 : bond 0.00654 / 0.34 ( 1) link_BETA1-4 : angle 1.10454 / 0.86 ( 3) link_NAG-ASN : bond 0.00143 / 0.08 ( 1) link_NAG-ASN : angle 0.94471 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: R 423 TYR cc_start: 0.8071 (t80) cc_final: 0.7721 (t80) REVERT: R 434 ILE cc_start: 0.8866 (mt) cc_final: 0.8482 (tt) REVERT: R 492 LEU cc_start: 0.8763 (mt) cc_final: 0.8487 (mp) REVERT: H 32 GLN cc_start: 0.6242 (mm-40) cc_final: 0.6026 (mm-40) REVERT: H 72 TYR cc_start: 0.7140 (p90) cc_final: 0.6625 (p90) REVERT: L 50 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7657 (tm-30) REVERT: L 74 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8474 (tt) REVERT: L 111 TYR cc_start: 0.8161 (m-80) cc_final: 0.7687 (m-80) REVERT: L 127 LYS cc_start: 0.8004 (tptp) cc_final: 0.7632 (mtmt) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.0514 time to fit residues: 7.5689 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.144694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120515 restraints weight = 5845.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124711 restraints weight = 3346.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127652 restraints weight = 2272.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129789 restraints weight = 1715.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131233 restraints weight = 1384.572| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3465 Z= 0.185 Angle : 0.827 13.657 4711 Z= 0.405 Chirality : 0.047 0.165 499 Planarity : 0.007 0.116 604 Dihedral : 6.621 47.999 481 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.59 % Favored : 87.92 % Rotamer: Outliers : 6.65 % Allowed : 24.65 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.67 (0.42), residues: 414 helix: -3.38 (0.84), residues: 18 sheet: -1.85 (0.44), residues: 137 loop : -1.61 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 91 TYR 0.015 0.002 TYR H 123 PHE 0.028 0.002 PHE H 133 TRP 0.032 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 3458) covalent geometry : angle 0.82352 / 0.40 ( 4695) SS BOND : bond 0.00261 / 0.15 ( 5) SS BOND : angle 1.70036 / 1.14 ( 10) hydrogen bonds : bond 0.03407 / 2.07 ( 74) hydrogen bonds : angle 7.31920 / 4.79 ( 183) link_BETA1-4 : bond 0.00382 / 0.20 ( 1) link_BETA1-4 : angle 1.09289 / 0.92 ( 3) link_NAG-ASN : bond 0.00002 / 0.00 ( 1) link_NAG-ASN : angle 1.02580 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: R 423 TYR cc_start: 0.8129 (t80) cc_final: 0.7874 (t80) REVERT: H 32 GLN cc_start: 0.6105 (mm-40) cc_final: 0.5860 (mm-40) REVERT: H 72 TYR cc_start: 0.7227 (p90) cc_final: 0.6685 (p90) REVERT: L 26 SER cc_start: 0.7741 (OUTLIER) cc_final: 0.7322 (p) REVERT: L 50 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7705 (tm-30) REVERT: L 74 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8595 (tt) REVERT: L 111 TYR cc_start: 0.8161 (m-80) cc_final: 0.7688 (m-80) REVERT: L 127 LYS cc_start: 0.8177 (tptp) cc_final: 0.7788 (mtmt) outliers start: 24 outliers final: 20 residues processed: 114 average time/residue: 0.0577 time to fit residues: 7.9843 Evaluate side-chains 111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.145317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121135 restraints weight = 5781.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125394 restraints weight = 3290.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128243 restraints weight = 2225.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.130424 restraints weight = 1686.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131934 restraints weight = 1356.790| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3465 Z= 0.168 Angle : 0.831 13.601 4711 Z= 0.405 Chirality : 0.047 0.149 499 Planarity : 0.006 0.114 604 Dihedral : 6.642 47.691 481 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.39 % Favored : 89.13 % Rotamer: Outliers : 6.65 % Allowed : 24.93 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.63 (0.42), residues: 414 helix: -3.37 (0.83), residues: 18 sheet: -1.85 (0.44), residues: 137 loop : -1.56 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 91 TYR 0.015 0.001 TYR H 123 PHE 0.028 0.002 PHE H 133 TRP 0.034 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 3458) covalent geometry : angle 0.82850 / 0.40 ( 4695) SS BOND : bond 0.00273 / 0.17 ( 5) SS BOND : angle 1.59408 / 1.06 ( 10) hydrogen bonds : bond 0.03386 / 2.06 ( 74) hydrogen bonds : angle 7.30723 / 4.76 ( 183) link_BETA1-4 : bond 0.00400 / 0.21 ( 1) link_BETA1-4 : angle 1.04957 / 0.87 ( 3) link_NAG-ASN : bond 0.00082 / 0.04 ( 1) link_NAG-ASN : angle 0.97743 / 0.64 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8083 (t80) cc_final: 0.7835 (t80) REVERT: R 434 ILE cc_start: 0.8907 (mt) cc_final: 0.8547 (tt) REVERT: H 32 GLN cc_start: 0.6060 (mm-40) cc_final: 0.5842 (mm-40) REVERT: L 26 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7718 (p) REVERT: L 50 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7693 (tm-30) REVERT: L 74 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8602 (tt) REVERT: L 111 TYR cc_start: 0.8175 (m-80) cc_final: 0.7702 (m-80) REVERT: L 127 LYS cc_start: 0.8122 (tptp) cc_final: 0.7798 (mtmt) outliers start: 24 outliers final: 21 residues processed: 106 average time/residue: 0.0620 time to fit residues: 7.9300 Evaluate side-chains 111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 487 ASN H 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123653 restraints weight = 5917.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.128094 restraints weight = 3346.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131203 restraints weight = 2238.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133279 restraints weight = 1662.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134567 restraints weight = 1337.318| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 3465 Z= 0.144 Angle : 0.828 13.605 4711 Z= 0.405 Chirality : 0.046 0.143 499 Planarity : 0.006 0.113 604 Dihedral : 6.549 47.272 481 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.14 % Favored : 89.37 % Rotamer: Outliers : 6.37 % Allowed : 25.21 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.55 (0.43), residues: 414 helix: -3.25 (0.87), residues: 18 sheet: -1.81 (0.44), residues: 138 loop : -1.51 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 91 TYR 0.014 0.001 TYR H 123 PHE 0.026 0.002 PHE H 133 TRP 0.034 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 3458) covalent geometry : angle 0.82575 / 0.40 ( 4695) SS BOND : bond 0.00264 / 0.17 ( 5) SS BOND : angle 1.59010 / 1.06 ( 10) hydrogen bonds : bond 0.03285 / 2.00 ( 74) hydrogen bonds : angle 7.21324 / 4.69 ( 183) link_BETA1-4 : bond 0.00447 / 0.24 ( 1) link_BETA1-4 : angle 1.04141 / 0.83 ( 3) link_NAG-ASN : bond 0.00131 / 0.07 ( 1) link_NAG-ASN : angle 0.96182 / 0.63 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 803.10 seconds wall clock time: 14 minutes 32.46 seconds (872.46 seconds total)