Starting phenix.real_space_refine on Wed Sep 17 03:45:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e21_47426/09_2025/9e21_47426.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e21_47426/09_2025/9e21_47426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e21_47426/09_2025/9e21_47426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e21_47426/09_2025/9e21_47426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e21_47426/09_2025/9e21_47426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e21_47426/09_2025/9e21_47426.map" } resolution = 3.1 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= 0.009 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 16 5.16 5 C 2097 2.51 5 N 553 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3285 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 882 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "S" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1601 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 15, 'TRANS': 185} Chain: "S" 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: 1.22, per 1000 atoms: 0.37 Number of scatterers: 3285 At special positions: 0 Unit cell: (59.4, 74.25, 108.075, 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 16 16.00 O 619 8.00 N 553 7.00 C 2097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS S 336 " - pdb=" SG CYS S 361 " distance=2.03 Simple disulfide: pdb=" SG CYS S 379 " - pdb=" SG CYS S 432 " distance=2.03 Simple disulfide: pdb=" SG CYS S 480 " - pdb=" SG CYS S 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG S 601 " - " ASN S 331 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 133.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 9.9% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.532A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.770A pdb=" N THR H 90 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 337 through 343 Processing helix chain 'S' and resid 383 through 390 removed outlier: 4.099A pdb=" N LEU S 387 " --> pdb=" O PRO S 384 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN S 388 " --> pdb=" O THR S 385 " (cutoff:3.500A) Processing helix chain 'S' and resid 406 through 410 Processing helix chain 'S' and resid 416 through 422 removed outlier: 3.525A pdb=" N ASP S 420 " --> pdb=" O GLY S 416 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR S 421 " --> pdb=" O ASN S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.112A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.989A pdb=" N PHE H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU H 99 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU H 105 " --> pdb=" O LEU H 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.757A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 354 through 358 removed outlier: 3.762A pdb=" N ASN S 394 " --> pdb=" O GLU S 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'S' and resid 473 through 474 114 hydrogen bonds defined for protein. 261 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: 0.53 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1045 1.34 - 1.46: 727 1.46 - 1.58: 1580 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3372 Sorted by residual: bond pdb=" C GLN H 110 " pdb=" N GLY H 111 " ideal model delta sigma weight residual 1.322 1.330 -0.008 1.20e-02 6.94e+03 4.70e-01 bond pdb=" CB PRO S 337 " pdb=" CG PRO S 337 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.89e-01 bond pdb=" CA CYS S 488 " pdb=" C CYS S 488 " ideal model delta sigma weight residual 1.526 1.520 0.006 1.03e-02 9.43e+03 3.75e-01 bond pdb=" CG PRO S 491 " pdb=" CD PRO S 491 " ideal model delta sigma weight residual 1.503 1.485 0.018 3.40e-02 8.65e+02 2.90e-01 bond pdb=" CB VAL S 350 " pdb=" CG2 VAL S 350 " ideal model delta sigma weight residual 1.521 1.505 0.016 3.30e-02 9.18e+02 2.40e-01 ... (remaining 3367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 4336 0.93 - 1.86: 193 1.86 - 2.79: 36 2.79 - 3.72: 15 3.72 - 4.65: 5 Bond angle restraints: 4585 Sorted by residual: angle pdb=" N GLY L 66 " pdb=" CA GLY L 66 " pdb=" C GLY L 66 " ideal model delta sigma weight residual 110.63 115.21 -4.58 1.45e+00 4.76e-01 9.98e+00 angle pdb=" C GLY L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.57 -4.03 1.91e+00 2.74e-01 4.46e+00 angle pdb=" C ARG H 100 " pdb=" N GLU H 101 " pdb=" CA GLU H 101 " ideal model delta sigma weight residual 121.54 125.49 -3.95 1.91e+00 2.74e-01 4.28e+00 angle pdb=" N LEU H 99 " pdb=" CA LEU H 99 " pdb=" C LEU H 99 " ideal model delta sigma weight residual 110.44 108.15 2.29 1.20e+00 6.94e-01 3.66e+00 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 112.47 108.96 3.51 2.06e+00 2.36e-01 2.91e+00 ... (remaining 4580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.36: 1770 14.36 - 28.73: 161 28.73 - 43.09: 51 43.09 - 57.45: 13 57.45 - 71.82: 5 Dihedral angle restraints: 2000 sinusoidal: 786 harmonic: 1214 Sorted by residual: dihedral pdb=" CB CYS S 480 " pdb=" SG CYS S 480 " pdb=" SG CYS S 488 " pdb=" CB CYS S 488 " ideal model delta sinusoidal sigma weight residual 93.00 156.17 -63.17 1 1.00e+01 1.00e-02 5.27e+01 dihedral pdb=" CA LEU L 94 " pdb=" C LEU L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB MET H 34 " pdb=" CG MET H 34 " pdb=" SD MET H 34 " pdb=" CE MET H 34 " ideal model delta sinusoidal sigma weight residual 60.00 119.79 -59.79 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 266 0.027 - 0.053: 145 0.053 - 0.080: 41 0.080 - 0.107: 27 0.107 - 0.133: 19 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ILE S 332 " pdb=" N ILE S 332 " pdb=" C ILE S 332 " pdb=" CB ILE S 332 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE S 358 " pdb=" N ILE S 358 " pdb=" C ILE S 358 " pdb=" CB ILE S 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 495 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 13 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO H 14 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS S 462 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO S 463 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO S 463 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO S 463 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 12 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO H 13 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 13 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 13 " 0.017 5.00e-02 4.00e+02 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1455 2.96 - 3.44: 2774 3.44 - 3.93: 5384 3.93 - 4.41: 6175 4.41 - 4.90: 10334 Nonbonded interactions: 26122 Sorted by model distance: nonbonded pdb=" CZ PHE H 58 " pdb=" CG2 THR S 415 " model vdw 2.470 3.760 nonbonded pdb=" OG SER H 56 " pdb=" OG1 THR S 415 " model vdw 2.590 3.040 nonbonded pdb=" C THR S 415 " pdb=" CG2 THR S 415 " model vdw 2.611 2.952 nonbonded pdb=" N LYS H 86 " pdb=" O LYS H 86 " model vdw 2.642 2.496 nonbonded pdb=" N ASP H 10 " pdb=" O ASP H 10 " model vdw 2.644 2.496 ... (remaining 26117 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: 8.650 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.620 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.002 0.031 3377 Z= 0.098 Angle : 0.494 4.649 4596 Z= 0.267 Chirality : 0.043 0.133 498 Planarity : 0.004 0.040 592 Dihedral : 12.991 71.816 1218 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.28 % Allowed : 0.84 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.39), residues: 418 helix: -3.96 (0.67), residues: 12 sheet: 0.08 (0.43), residues: 126 loop : -1.00 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 66 TYR 0.012 0.001 TYR H 33 PHE 0.009 0.001 PHE S 455 TRP 0.008 0.001 TRP H 108 HIS 0.002 0.000 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 3372) covalent geometry : angle 0.49216 ( 4585) SS BOND : bond 0.00165 ( 4) SS BOND : angle 1.04579 ( 8) hydrogen bonds : bond 0.13478 ( 109) hydrogen bonds : angle 7.01512 ( 261) link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 0.81470 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.129 Fit side-chains REVERT: H 32 ASN cc_start: 0.7928 (m-40) cc_final: 0.7641 (m110) REVERT: H 35 THR cc_start: 0.8405 (p) cc_final: 0.8134 (m) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.0591 time to fit residues: 5.3019 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.0670 chunk 16 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 0.2980 overall best weight: 0.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 ASN S 388 ASN S 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102076 restraints weight = 4873.842| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.88 r_work: 0.3119 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3377 Z= 0.121 Angle : 0.505 7.067 4596 Z= 0.258 Chirality : 0.044 0.130 498 Planarity : 0.004 0.039 592 Dihedral : 4.226 19.716 483 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.39), residues: 418 helix: -3.84 (0.60), residues: 21 sheet: 0.19 (0.43), residues: 127 loop : -0.74 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 66 TYR 0.019 0.001 TYR S 495 PHE 0.036 0.001 PHE S 455 TRP 0.009 0.001 TRP S 353 HIS 0.003 0.001 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3372) covalent geometry : angle 0.50261 ( 4585) SS BOND : bond 0.00401 ( 4) SS BOND : angle 1.18263 ( 8) hydrogen bonds : bond 0.03090 ( 109) hydrogen bonds : angle 5.83235 ( 261) link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 0.92593 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.151 Fit side-chains REVERT: H 32 ASN cc_start: 0.7980 (m-40) cc_final: 0.7678 (m110) REVERT: H 117 SER cc_start: 0.7844 (t) cc_final: 0.7617 (m) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0614 time to fit residues: 3.9225 Evaluate side-chains 46 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 38 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.0870 chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100422 restraints weight = 4867.336| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.83 r_work: 0.3087 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 3377 Z= 0.199 Angle : 0.545 6.155 4596 Z= 0.281 Chirality : 0.045 0.131 498 Planarity : 0.005 0.041 592 Dihedral : 4.643 21.965 483 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.84 % Allowed : 8.66 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.39), residues: 418 helix: -3.54 (0.69), residues: 21 sheet: 0.06 (0.42), residues: 132 loop : -0.76 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 466 TYR 0.025 0.002 TYR S 495 PHE 0.031 0.002 PHE S 455 TRP 0.014 0.002 TRP S 353 HIS 0.006 0.001 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 3372) covalent geometry : angle 0.54223 ( 4585) SS BOND : bond 0.00451 ( 4) SS BOND : angle 1.27650 ( 8) hydrogen bonds : bond 0.03398 ( 109) hydrogen bonds : angle 6.01174 ( 261) link_NAG-ASN : bond 0.00514 ( 1) link_NAG-ASN : angle 1.12006 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.132 Fit side-chains REVERT: H 117 SER cc_start: 0.7881 (t) cc_final: 0.7640 (m) REVERT: S 371 PHE cc_start: 0.7328 (m-80) cc_final: 0.6888 (m-80) outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.0651 time to fit residues: 3.9426 Evaluate side-chains 46 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain S residue 332 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 40 optimal weight: 0.0570 chunk 32 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN S 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099308 restraints weight = 4824.625| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.93 r_work: 0.3058 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3377 Z= 0.224 Angle : 0.557 5.314 4596 Z= 0.288 Chirality : 0.046 0.133 498 Planarity : 0.005 0.043 592 Dihedral : 4.782 22.635 483 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.68 % Allowed : 9.78 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.39), residues: 418 helix: -3.45 (0.71), residues: 21 sheet: -0.01 (0.42), residues: 132 loop : -0.84 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 466 TYR 0.025 0.002 TYR S 495 PHE 0.033 0.002 PHE S 455 TRP 0.014 0.002 TRP S 353 HIS 0.005 0.001 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 3372) covalent geometry : angle 0.55392 ( 4585) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.33417 ( 8) hydrogen bonds : bond 0.03411 ( 109) hydrogen bonds : angle 6.06853 ( 261) link_NAG-ASN : bond 0.00613 ( 1) link_NAG-ASN : angle 1.12280 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.134 Fit side-chains REVERT: H 82 MET cc_start: 0.8405 (mtm) cc_final: 0.8036 (mtp) REVERT: H 117 SER cc_start: 0.7905 (t) cc_final: 0.7641 (m) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.0454 time to fit residues: 3.0159 Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain S residue 332 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.2980 chunk 39 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.0670 chunk 37 optimal weight: 0.0010 chunk 33 optimal weight: 0.2980 chunk 38 optimal weight: 0.0770 overall best weight: 0.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102028 restraints weight = 4826.770| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.95 r_work: 0.3098 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3377 Z= 0.098 Angle : 0.477 4.369 4596 Z= 0.247 Chirality : 0.043 0.134 498 Planarity : 0.004 0.042 592 Dihedral : 4.203 19.662 483 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.12 % Allowed : 10.61 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.39), residues: 418 helix: -3.27 (0.79), residues: 21 sheet: 0.10 (0.43), residues: 129 loop : -0.84 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 466 TYR 0.014 0.001 TYR S 495 PHE 0.033 0.001 PHE S 455 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.000 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 3372) covalent geometry : angle 0.47533 ( 4585) SS BOND : bond 0.00305 ( 4) SS BOND : angle 1.05110 ( 8) hydrogen bonds : bond 0.02810 ( 109) hydrogen bonds : angle 5.60277 ( 261) link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 0.86808 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.130 Fit side-chains REVERT: H 82 MET cc_start: 0.8343 (mtm) cc_final: 0.7913 (mtp) REVERT: H 117 SER cc_start: 0.7777 (t) cc_final: 0.7537 (m) REVERT: L 47 LEU cc_start: 0.8186 (mt) cc_final: 0.7938 (mt) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.0580 time to fit residues: 3.8189 Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.0040 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN S 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100148 restraints weight = 4815.182| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.94 r_work: 0.3073 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3377 Z= 0.180 Angle : 0.529 6.147 4596 Z= 0.272 Chirality : 0.045 0.132 498 Planarity : 0.005 0.042 592 Dihedral : 4.524 21.519 483 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.12 % Allowed : 11.45 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.39), residues: 418 helix: -3.09 (0.83), residues: 21 sheet: 0.21 (0.44), residues: 127 loop : -0.82 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 466 TYR 0.023 0.002 TYR S 495 PHE 0.026 0.002 PHE S 455 TRP 0.012 0.002 TRP S 353 HIS 0.004 0.001 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3372) covalent geometry : angle 0.52585 ( 4585) SS BOND : bond 0.00469 ( 4) SS BOND : angle 1.44090 ( 8) hydrogen bonds : bond 0.03150 ( 109) hydrogen bonds : angle 5.77449 ( 261) link_NAG-ASN : bond 0.00461 ( 1) link_NAG-ASN : angle 1.04493 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.114 Fit side-chains REVERT: H 32 ASN cc_start: 0.8102 (m-40) cc_final: 0.7786 (m110) REVERT: H 82 MET cc_start: 0.8354 (mtm) cc_final: 0.7947 (mtp) REVERT: H 115 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7889 (m) REVERT: H 117 SER cc_start: 0.7870 (t) cc_final: 0.7610 (m) REVERT: S 474 GLN cc_start: 0.8186 (tt0) cc_final: 0.7947 (tt0) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.0564 time to fit residues: 3.9024 Evaluate side-chains 51 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 22 optimal weight: 0.0670 chunk 9 optimal weight: 0.1980 chunk 21 optimal weight: 0.0980 chunk 24 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 28 optimal weight: 0.1980 overall best weight: 0.0728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103376 restraints weight = 4966.034| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.87 r_work: 0.3134 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3377 Z= 0.079 Angle : 0.470 6.838 4596 Z= 0.237 Chirality : 0.043 0.135 498 Planarity : 0.004 0.041 592 Dihedral : 3.955 18.483 483 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.84 % Allowed : 11.45 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.40), residues: 418 helix: -2.94 (0.90), residues: 21 sheet: 0.33 (0.44), residues: 129 loop : -0.67 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 328 TYR 0.011 0.001 TYR H 33 PHE 0.028 0.001 PHE S 455 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.000 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 3372) covalent geometry : angle 0.46726 ( 4585) SS BOND : bond 0.00286 ( 4) SS BOND : angle 1.18632 ( 8) hydrogen bonds : bond 0.02613 ( 109) hydrogen bonds : angle 5.33834 ( 261) link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 0.87194 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.119 Fit side-chains REVERT: H 32 ASN cc_start: 0.7883 (m-40) cc_final: 0.7632 (m110) REVERT: L 4 MET cc_start: 0.8620 (mtp) cc_final: 0.8406 (mmm) REVERT: S 437 ASN cc_start: 0.8243 (t0) cc_final: 0.7991 (t0) REVERT: S 474 GLN cc_start: 0.8137 (tt0) cc_final: 0.7900 (tt0) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.0554 time to fit residues: 4.2684 Evaluate side-chains 52 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 11 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099730 restraints weight = 4906.897| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.97 r_work: 0.3061 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 3377 Z= 0.195 Angle : 0.545 7.619 4596 Z= 0.278 Chirality : 0.045 0.130 498 Planarity : 0.005 0.041 592 Dihedral : 4.540 21.323 483 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.40 % Allowed : 12.29 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.40), residues: 418 helix: -3.00 (0.88), residues: 21 sheet: 0.35 (0.44), residues: 125 loop : -0.74 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 466 TYR 0.023 0.002 TYR S 495 PHE 0.013 0.002 PHE S 347 TRP 0.014 0.002 TRP S 353 HIS 0.005 0.001 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 3372) covalent geometry : angle 0.54026 ( 4585) SS BOND : bond 0.00522 ( 4) SS BOND : angle 1.65956 ( 8) hydrogen bonds : bond 0.03182 ( 109) hydrogen bonds : angle 5.74295 ( 261) link_NAG-ASN : bond 0.00563 ( 1) link_NAG-ASN : angle 1.07694 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.131 Fit side-chains REVERT: H 32 ASN cc_start: 0.8106 (m-40) cc_final: 0.7785 (m110) REVERT: H 115 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7853 (m) REVERT: H 117 SER cc_start: 0.7927 (t) cc_final: 0.7600 (m) REVERT: S 474 GLN cc_start: 0.8177 (tt0) cc_final: 0.7924 (tt0) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.0634 time to fit residues: 3.9748 Evaluate side-chains 47 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.2980 chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 0.0980 chunk 1 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 overall best weight: 0.1156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101078 restraints weight = 4857.973| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.00 r_work: 0.3095 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3377 Z= 0.093 Angle : 0.486 7.558 4596 Z= 0.245 Chirality : 0.043 0.135 498 Planarity : 0.004 0.041 592 Dihedral : 4.072 19.299 483 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.84 % Allowed : 13.13 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.40), residues: 418 helix: -2.94 (0.90), residues: 21 sheet: 0.33 (0.44), residues: 129 loop : -0.70 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 466 TYR 0.013 0.001 TYR S 495 PHE 0.009 0.001 PHE S 455 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.000 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3372) covalent geometry : angle 0.48324 ( 4585) SS BOND : bond 0.00216 ( 4) SS BOND : angle 1.34701 ( 8) hydrogen bonds : bond 0.02711 ( 109) hydrogen bonds : angle 5.44732 ( 261) link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 0.90624 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.132 Fit side-chains REVERT: H 32 ASN cc_start: 0.7978 (m-40) cc_final: 0.7731 (m110) REVERT: H 117 SER cc_start: 0.7867 (t) cc_final: 0.7549 (m) REVERT: L 4 MET cc_start: 0.8676 (mtp) cc_final: 0.8325 (mmm) REVERT: L 47 LEU cc_start: 0.8191 (mt) cc_final: 0.7943 (mt) REVERT: S 437 ASN cc_start: 0.8332 (t0) cc_final: 0.8115 (t0) REVERT: S 474 GLN cc_start: 0.8182 (tt0) cc_final: 0.7929 (tt0) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.0721 time to fit residues: 4.8349 Evaluate side-chains 50 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099753 restraints weight = 4819.377| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.95 r_work: 0.3078 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3377 Z= 0.161 Angle : 0.524 7.296 4596 Z= 0.267 Chirality : 0.045 0.131 498 Planarity : 0.004 0.041 592 Dihedral : 4.366 20.774 483 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.40 % Allowed : 12.85 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.40), residues: 418 helix: -2.94 (0.90), residues: 21 sheet: 0.32 (0.45), residues: 127 loop : -0.75 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 466 TYR 0.021 0.001 TYR S 495 PHE 0.012 0.001 PHE S 347 TRP 0.012 0.002 TRP S 353 HIS 0.004 0.001 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3372) covalent geometry : angle 0.51903 ( 4585) SS BOND : bond 0.00394 ( 4) SS BOND : angle 1.64960 ( 8) hydrogen bonds : bond 0.03003 ( 109) hydrogen bonds : angle 5.66643 ( 261) link_NAG-ASN : bond 0.00401 ( 1) link_NAG-ASN : angle 0.99740 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.131 Fit side-chains REVERT: H 32 ASN cc_start: 0.8071 (m-40) cc_final: 0.7811 (m110) REVERT: H 115 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7838 (m) REVERT: H 117 SER cc_start: 0.7920 (t) cc_final: 0.7597 (m) REVERT: L 4 MET cc_start: 0.8697 (mtp) cc_final: 0.8298 (mmm) REVERT: S 474 GLN cc_start: 0.8178 (tt0) cc_final: 0.7924 (tt0) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.0639 time to fit residues: 4.2154 Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 14 optimal weight: 0.0030 chunk 29 optimal weight: 0.0050 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100550 restraints weight = 4878.980| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.00 r_work: 0.3113 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3377 Z= 0.108 Angle : 0.493 7.269 4596 Z= 0.249 Chirality : 0.043 0.134 498 Planarity : 0.004 0.040 592 Dihedral : 4.123 19.745 483 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.40 % Allowed : 12.85 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.40), residues: 418 helix: -2.97 (0.90), residues: 21 sheet: 0.35 (0.45), residues: 127 loop : -0.69 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 509 TYR 0.015 0.001 TYR S 495 PHE 0.010 0.001 PHE S 455 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.000 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3372) covalent geometry : angle 0.48948 ( 4585) SS BOND : bond 0.00285 ( 4) SS BOND : angle 1.39105 ( 8) hydrogen bonds : bond 0.02761 ( 109) hydrogen bonds : angle 5.51236 ( 261) link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 0.94233 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1361.98 seconds wall clock time: 24 minutes 6.48 seconds (1446.48 seconds total)