Starting phenix.real_space_refine on Thu Jul 2 01:13:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12qj_76684/07_2026/12qj_76684.cif Found real_map, /net/cci-nas-00/data/ceres_data/12qj_76684/07_2026/12qj_76684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12qj_76684/07_2026/12qj_76684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12qj_76684/07_2026/12qj_76684.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12qj_76684/07_2026/12qj_76684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12qj_76684/07_2026/12qj_76684.map" } resolution = 3.35 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= -0.001 sd= 0.039 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 9 5.16 5 C 3150 2.51 5 N 857 2.21 5 O 971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 4987 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3222 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 9, 'TRANS': 384} Chain: "B" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Time building chain proxies: 1.48, per 1000 atoms: 0.30 Number of scatterers: 4987 At special positions: 0 Unit cell: (62.41, 77.42, 114.55, 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 9 16.00 O 971 8.00 N 857 7.00 C 3150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.04 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 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 196.3 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 12.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 122 through 138 removed outlier: 4.163A pdb=" N GLY A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 Proline residue: A 214 - end of helix removed outlier: 4.150A pdb=" N GLY A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.879A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 4.360A pdb=" N LYS A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 271 " --> pdb=" O TRP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.314A pdb=" N GLY A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 3.883A pdb=" N LEU A 21 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 28 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.756A pdb=" N ILE A 79 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 104 " --> pdb=" O SER A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 313 removed outlier: 3.894A pdb=" N TRP A 321 " --> pdb=" O HIS A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 338 removed outlier: 7.983A pdb=" N TYR A 344 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A 351 " --> pdb=" O TYR A 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.825A pdb=" N LYS A 357 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 364 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.761A pdb=" N PHE B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.284A pdb=" N TRP B 48 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG B 39 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 50 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 93 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.827A pdb=" N ILE C 77 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.679A pdb=" N ILE C 50 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 40 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP C 87 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 99 " --> pdb=" O ASP C 94 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 192 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: 0.79 Time building geometry restraints manager: 0.56 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: 1627 1.34 - 1.46: 1308 1.46 - 1.58: 2168 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 5117 Sorted by residual: bond pdb=" CA ASP A 252 " pdb=" CB ASP A 252 " ideal model delta sigma weight residual 1.527 1.565 -0.037 2.48e-02 1.63e+03 2.28e+00 bond pdb=" CA ASN A 225 " pdb=" C ASN A 225 " ideal model delta sigma weight residual 1.531 1.515 0.016 1.39e-02 5.18e+03 1.38e+00 bond pdb=" CG1 ILE A 79 " pdb=" CD1 ILE A 79 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CA ASN A 360 " pdb=" CB ASN A 360 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.70e-02 3.46e+03 1.14e+00 bond pdb=" C GLY B 8 " pdb=" N PRO B 9 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.12e+00 ... (remaining 5112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 6647 1.92 - 3.84: 254 3.84 - 5.76: 41 5.76 - 7.68: 7 7.68 - 9.60: 7 Bond angle restraints: 6956 Sorted by residual: angle pdb=" N SER B 103 " pdb=" CA SER B 103 " pdb=" C SER B 103 " ideal model delta sigma weight residual 108.07 101.74 6.33 8.90e-01 1.26e+00 5.06e+01 angle pdb=" CA SER B 103 " pdb=" C SER B 103 " pdb=" N PRO B 104 " ideal model delta sigma weight residual 117.82 121.84 -4.02 7.80e-01 1.64e+00 2.65e+01 angle pdb=" C SER B 103 " pdb=" CA SER B 103 " pdb=" CB SER B 103 " ideal model delta sigma weight residual 110.76 116.94 -6.18 1.22e+00 6.72e-01 2.57e+01 angle pdb=" C ILE C 64 " pdb=" N SER C 65 " pdb=" CA SER C 65 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" C ARG B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta sigma weight residual 121.90 116.85 5.05 1.26e+00 6.30e-01 1.61e+01 ... (remaining 6951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2462 17.76 - 35.52: 375 35.52 - 53.28: 108 53.28 - 71.04: 22 71.04 - 88.80: 5 Dihedral angle restraints: 2972 sinusoidal: 1169 harmonic: 1803 Sorted by residual: dihedral pdb=" CA SER B 103 " pdb=" C SER B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual -180.00 -138.84 -41.16 0 5.00e+00 4.00e-02 6.78e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual -86.00 -132.61 46.61 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA VAL A 188 " pdb=" C VAL A 188 " pdb=" N VAL A 189 " pdb=" CA VAL A 189 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 2969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 504 0.045 - 0.091: 167 0.091 - 0.136: 57 0.136 - 0.181: 7 0.181 - 0.227: 2 Chirality restraints: 737 Sorted by residual: chirality pdb=" CB ILE C 20 " pdb=" CA ILE C 20 " pdb=" CG1 ILE C 20 " pdb=" CG2 ILE C 20 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 189 " pdb=" CA VAL A 189 " pdb=" CG1 VAL A 189 " pdb=" CG2 VAL A 189 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA PHE A 65 " pdb=" N PHE A 65 " pdb=" C PHE A 65 " pdb=" CB PHE A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 734 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 103 " 0.098 5.00e-02 4.00e+02 1.48e-01 3.52e+01 pdb=" N PRO B 104 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 61 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C THR A 61 " -0.062 2.00e-02 2.50e+03 pdb=" O THR A 61 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 62 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 99 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 100 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " -0.032 5.00e-02 4.00e+02 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 2371 2.93 - 3.42: 5022 3.42 - 3.91: 8661 3.91 - 4.41: 9974 4.41 - 4.90: 16225 Nonbonded interactions: 42253 Sorted by model distance: nonbonded pdb=" N SER B 103 " pdb=" O SER B 103 " model vdw 2.433 2.496 nonbonded pdb=" O ASN A 360 " pdb=" OD1 ASN A 360 " model vdw 2.528 3.040 nonbonded pdb=" O LEU A 124 " pdb=" OD2 ASP A 128 " model vdw 2.541 3.040 nonbonded pdb=" N ASN A 225 " pdb=" O ASN A 225 " model vdw 2.552 2.496 nonbonded pdb=" O GLY A 200 " pdb=" OD1 ASP A 201 " model vdw 2.552 3.040 ... (remaining 42248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.800 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 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 : 0.004 0.047 5119 Z= 0.186 Angle : 0.892 9.595 6960 Z= 0.501 Chirality : 0.051 0.227 737 Planarity : 0.007 0.148 898 Dihedral : 18.618 88.800 1822 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.80 % Allowed : 16.19 % Favored : 83.01 % Rotamer: Outliers : 4.79 % Allowed : 33.33 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.85 (0.28), residues: 624 helix: -3.06 (0.47), residues: 57 sheet: -3.77 (0.43), residues: 98 loop : -3.39 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 45 TYR 0.014 0.002 TYR A 105 PHE 0.017 0.003 PHE B 79 TRP 0.025 0.002 TRP A 320 HIS 0.005 0.002 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 ( 5117) covalent geometry : angle 0.89096 / 0.50 ( 6956) SS BOND : bond 0.00602 / 0.29 ( 2) SS BOND : angle 1.68271 / 0.83 ( 4) hydrogen bonds : bond 0.20128 / 14.36 ( 74) hydrogen bonds : angle 10.98715 / 7.52 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.6565 (OUTLIER) cc_final: 0.5945 (m-90) REVERT: A 224 PHE cc_start: 0.6171 (OUTLIER) cc_final: 0.5661 (m-80) REVERT: A 229 ASP cc_start: 0.6380 (t0) cc_final: 0.6180 (t0) REVERT: A 392 MET cc_start: 0.4693 (tpt) cc_final: 0.4124 (ttp) REVERT: C 63 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.5297 (pmt-80) outliers start: 26 outliers final: 17 residues processed: 89 average time/residue: 0.0839 time to fit residues: 9.5616 Evaluate side-chains 78 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 63 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.204625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.181727 restraints weight = 6748.928| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.20 r_work: 0.4241 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5119 Z= 0.173 Angle : 0.787 8.675 6960 Z= 0.409 Chirality : 0.048 0.277 737 Planarity : 0.007 0.147 898 Dihedral : 9.569 58.986 732 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.80 % Allowed : 17.95 % Favored : 81.25 % Rotamer: Outliers : 7.18 % Allowed : 33.15 % Favored : 59.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.73 (0.28), residues: 624 helix: -2.97 (0.49), residues: 53 sheet: -3.70 (0.38), residues: 125 loop : -3.22 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.029 0.002 TYR A 322 PHE 0.017 0.003 PHE C 53 TRP 0.013 0.002 TRP B 48 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 5117) covalent geometry : angle 0.78531 / 0.41 ( 6956) SS BOND : bond 0.00509 / 0.26 ( 2) SS BOND : angle 2.13620 / 1.06 ( 4) hydrogen bonds : bond 0.04087 / 2.89 ( 74) hydrogen bonds : angle 8.51763 / 5.83 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 69 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.5292 (OUTLIER) cc_final: 0.4857 (m-30) REVERT: A 121 TRP cc_start: 0.6499 (OUTLIER) cc_final: 0.5567 (m-90) REVERT: A 129 LYS cc_start: 0.5233 (pttt) cc_final: 0.4966 (tttp) REVERT: A 224 PHE cc_start: 0.6564 (OUTLIER) cc_final: 0.5970 (m-80) REVERT: A 392 MET cc_start: 0.4456 (tpt) cc_final: 0.3755 (ttp) REVERT: B 39 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.5273 (ptm-80) outliers start: 39 outliers final: 27 residues processed: 99 average time/residue: 0.0796 time to fit residues: 10.3538 Evaluate side-chains 95 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 49 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 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 = 0.4557 r_free = 0.4557 target = 0.200216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177205 restraints weight = 6717.429| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.19 r_work: 0.4220 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5119 Z= 0.196 Angle : 0.786 8.501 6960 Z= 0.408 Chirality : 0.048 0.232 737 Planarity : 0.007 0.142 898 Dihedral : 9.273 55.967 723 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.80 % Allowed : 18.27 % Favored : 80.93 % Rotamer: Outliers : 8.47 % Allowed : 31.68 % Favored : 59.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.66 (0.29), residues: 624 helix: -2.80 (0.51), residues: 54 sheet: -3.56 (0.39), residues: 125 loop : -3.22 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.016 0.002 TYR A 322 PHE 0.018 0.003 PHE C 53 TRP 0.013 0.002 TRP B 48 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 5117) covalent geometry : angle 0.78504 / 0.41 ( 6956) SS BOND : bond 0.01058 / 0.51 ( 2) SS BOND : angle 1.70492 / 0.86 ( 4) hydrogen bonds : bond 0.04084 / 2.93 ( 74) hydrogen bonds : angle 8.22389 / 5.62 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 71 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.5313 (OUTLIER) cc_final: 0.4838 (m-30) REVERT: A 121 TRP cc_start: 0.6558 (OUTLIER) cc_final: 0.5936 (m-90) REVERT: A 129 LYS cc_start: 0.5385 (pttt) cc_final: 0.4838 (tttp) REVERT: A 224 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: A 275 ARG cc_start: 0.4833 (OUTLIER) cc_final: 0.4215 (tmm160) REVERT: A 392 MET cc_start: 0.4324 (tpt) cc_final: 0.3736 (ttp) REVERT: B 39 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5346 (ptm-80) REVERT: C 63 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.5822 (pmt-80) outliers start: 46 outliers final: 32 residues processed: 107 average time/residue: 0.0799 time to fit residues: 10.9494 Evaluate side-chains 105 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 67 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 63 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.206066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.183102 restraints weight = 6635.091| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.22 r_work: 0.4257 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5119 Z= 0.137 Angle : 0.716 8.507 6960 Z= 0.368 Chirality : 0.047 0.231 737 Planarity : 0.006 0.138 898 Dihedral : 8.654 57.971 719 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.80 % Allowed : 16.35 % Favored : 82.85 % Rotamer: Outliers : 7.73 % Allowed : 31.86 % Favored : 60.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.46 (0.29), residues: 624 helix: -2.42 (0.53), residues: 56 sheet: -3.39 (0.39), residues: 125 loop : -3.11 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.010 0.001 TYR A 331 PHE 0.016 0.002 PHE C 53 TRP 0.013 0.001 TRP B 48 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 5117) covalent geometry : angle 0.71570 / 0.37 ( 6956) SS BOND : bond 0.00705 / 0.34 ( 2) SS BOND : angle 0.86010 / 0.45 ( 4) hydrogen bonds : bond 0.03270 / 2.29 ( 74) hydrogen bonds : angle 7.71603 / 5.23 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 74 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 108 LYS cc_start: 0.7356 (tttm) cc_final: 0.6956 (mttm) REVERT: A 121 TRP cc_start: 0.6444 (OUTLIER) cc_final: 0.5928 (m-90) REVERT: A 129 LYS cc_start: 0.5253 (pttt) cc_final: 0.4619 (tttp) REVERT: A 222 MET cc_start: 0.7711 (tmm) cc_final: 0.7377 (tpt) REVERT: A 224 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.5808 (m-80) REVERT: A 275 ARG cc_start: 0.4718 (OUTLIER) cc_final: 0.4291 (tmm160) REVERT: A 376 TRP cc_start: 0.3699 (OUTLIER) cc_final: 0.3154 (p90) REVERT: A 392 MET cc_start: 0.4237 (tpt) cc_final: 0.3621 (ttp) REVERT: B 39 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5170 (ptm-80) REVERT: C 63 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.5928 (pmt-80) REVERT: C 93 HIS cc_start: 0.7208 (t-90) cc_final: 0.6957 (t-170) outliers start: 42 outliers final: 27 residues processed: 108 average time/residue: 0.0736 time to fit residues: 10.2600 Evaluate side-chains 104 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 TRP Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 95 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.206207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.183372 restraints weight = 6640.662| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.19 r_work: 0.4260 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5119 Z= 0.140 Angle : 0.724 11.583 6960 Z= 0.367 Chirality : 0.047 0.195 737 Planarity : 0.006 0.137 898 Dihedral : 8.360 59.391 717 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.80 % Allowed : 16.19 % Favored : 83.01 % Rotamer: Outliers : 8.10 % Allowed : 33.33 % Favored : 58.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.28 (0.30), residues: 624 helix: -2.21 (0.55), residues: 56 sheet: -3.29 (0.39), residues: 125 loop : -3.00 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 362 TYR 0.036 0.002 TYR A 322 PHE 0.016 0.002 PHE C 53 TRP 0.012 0.001 TRP B 48 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 5117) covalent geometry : angle 0.72352 / 0.37 ( 6956) SS BOND : bond 0.00782 / 0.38 ( 2) SS BOND : angle 0.75565 / 0.40 ( 4) hydrogen bonds : bond 0.03294 / 2.30 ( 74) hydrogen bonds : angle 7.53336 / 5.09 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 70 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.5169 (OUTLIER) cc_final: 0.4768 (m-30) REVERT: A 95 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 108 LYS cc_start: 0.7308 (tttm) cc_final: 0.6905 (mttm) REVERT: A 121 TRP cc_start: 0.6488 (OUTLIER) cc_final: 0.5998 (m-90) REVERT: A 129 LYS cc_start: 0.5160 (pttt) cc_final: 0.4745 (tttp) REVERT: A 222 MET cc_start: 0.7692 (tmm) cc_final: 0.7371 (tpt) REVERT: A 224 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5824 (m-80) REVERT: A 230 THR cc_start: 0.4761 (OUTLIER) cc_final: 0.4239 (p) REVERT: A 275 ARG cc_start: 0.4749 (OUTLIER) cc_final: 0.4371 (tmm160) REVERT: A 376 TRP cc_start: 0.3494 (OUTLIER) cc_final: 0.2945 (p90) REVERT: A 392 MET cc_start: 0.4127 (tpt) cc_final: 0.3573 (ttp) REVERT: B 39 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5182 (ptm-80) REVERT: C 63 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.5868 (pmt-80) REVERT: C 93 HIS cc_start: 0.7273 (t-90) cc_final: 0.7036 (t-170) outliers start: 44 outliers final: 30 residues processed: 105 average time/residue: 0.0756 time to fit residues: 10.2244 Evaluate side-chains 103 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 376 TRP Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 95 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 0.0070 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.206433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.183264 restraints weight = 6702.298| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.23 r_work: 0.4252 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 5119 Z= 0.142 Angle : 0.716 10.909 6960 Z= 0.367 Chirality : 0.049 0.338 737 Planarity : 0.006 0.137 898 Dihedral : 8.310 57.513 717 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.64 % Allowed : 16.19 % Favored : 83.17 % Rotamer: Outliers : 8.10 % Allowed : 34.62 % Favored : 57.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.20 (0.30), residues: 624 helix: -2.27 (0.53), residues: 53 sheet: -3.15 (0.40), residues: 125 loop : -2.95 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.024 0.001 TYR A 322 PHE 0.014 0.002 PHE C 53 TRP 0.020 0.001 TRP C 37 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5117) covalent geometry : angle 0.71649 / 0.37 ( 6956) SS BOND : bond 0.00771 / 0.37 ( 2) SS BOND : angle 0.66539 / 0.35 ( 4) hydrogen bonds : bond 0.03454 / 2.42 ( 74) hydrogen bonds : angle 7.38635 / 5.03 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 68 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.5377 (OUTLIER) cc_final: 0.4968 (m-30) REVERT: A 88 HIS cc_start: 0.5055 (m-70) cc_final: 0.4578 (m-70) REVERT: A 95 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8102 (mp) REVERT: A 108 LYS cc_start: 0.7355 (tttm) cc_final: 0.6935 (mttm) REVERT: A 121 TRP cc_start: 0.6474 (OUTLIER) cc_final: 0.5762 (m-90) REVERT: A 129 LYS cc_start: 0.5142 (pttt) cc_final: 0.4695 (tttp) REVERT: A 222 MET cc_start: 0.7700 (tmm) cc_final: 0.7426 (tpt) REVERT: A 224 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5709 (m-80) REVERT: A 376 TRP cc_start: 0.3491 (OUTLIER) cc_final: 0.2930 (p90) REVERT: A 392 MET cc_start: 0.4037 (tpt) cc_final: 0.3552 (ttp) REVERT: B 39 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5194 (ptm-80) REVERT: C 49 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4600 (mt) outliers start: 44 outliers final: 28 residues processed: 104 average time/residue: 0.0776 time to fit residues: 10.4601 Evaluate side-chains 99 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 TRP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 95 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 0.0370 chunk 59 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** 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 = 0.4587 r_free = 0.4587 target = 0.204872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.181769 restraints weight = 6608.204| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.22 r_work: 0.4241 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 5119 Z= 0.159 Angle : 0.745 10.437 6960 Z= 0.383 Chirality : 0.049 0.269 737 Planarity : 0.006 0.136 898 Dihedral : 8.165 57.235 715 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.64 % Allowed : 17.15 % Favored : 82.21 % Rotamer: Outliers : 7.37 % Allowed : 34.81 % Favored : 57.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.17 (0.30), residues: 624 helix: -2.27 (0.54), residues: 53 sheet: -3.14 (0.41), residues: 127 loop : -2.92 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 56 TYR 0.018 0.002 TYR A 322 PHE 0.024 0.002 PHE C 53 TRP 0.024 0.001 TRP C 37 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 5117) covalent geometry : angle 0.74531 / 0.38 ( 6956) SS BOND : bond 0.00736 / 0.36 ( 2) SS BOND : angle 0.74429 / 0.39 ( 4) hydrogen bonds : bond 0.03657 / 2.61 ( 74) hydrogen bonds : angle 7.15616 / 4.92 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 66 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.5452 (OUTLIER) cc_final: 0.5027 (m-30) REVERT: A 95 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 108 LYS cc_start: 0.7399 (tttm) cc_final: 0.6979 (mttm) REVERT: A 121 TRP cc_start: 0.6441 (OUTLIER) cc_final: 0.5711 (m-90) REVERT: A 129 LYS cc_start: 0.5218 (pttt) cc_final: 0.4697 (tttp) REVERT: A 222 MET cc_start: 0.7612 (tmm) cc_final: 0.7270 (tpt) REVERT: A 224 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.5794 (m-80) REVERT: A 230 THR cc_start: 0.4889 (OUTLIER) cc_final: 0.4379 (p) REVERT: A 392 MET cc_start: 0.3932 (tpt) cc_final: 0.3512 (ttp) REVERT: B 39 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.5210 (ptm-80) REVERT: C 49 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.4694 (mt) outliers start: 40 outliers final: 28 residues processed: 98 average time/residue: 0.0712 time to fit residues: 9.1209 Evaluate side-chains 97 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 95 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** 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 = 0.4613 r_free = 0.4613 target = 0.206158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.182618 restraints weight = 6779.408| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.25 r_work: 0.4266 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 5119 Z= 0.165 Angle : 0.758 9.810 6960 Z= 0.387 Chirality : 0.049 0.267 737 Planarity : 0.006 0.137 898 Dihedral : 8.222 58.541 715 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.64 % Allowed : 18.59 % Favored : 80.77 % Rotamer: Outliers : 6.63 % Allowed : 35.17 % Favored : 58.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.19 (0.30), residues: 624 helix: -2.30 (0.54), residues: 53 sheet: -2.93 (0.43), residues: 128 loop : -3.00 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 56 TYR 0.019 0.002 TYR A 322 PHE 0.015 0.002 PHE C 53 TRP 0.028 0.002 TRP A 335 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 5117) covalent geometry : angle 0.75821 / 0.39 ( 6956) SS BOND : bond 0.01178 / 0.57 ( 2) SS BOND : angle 0.87211 / 0.44 ( 4) hydrogen bonds : bond 0.03505 / 2.47 ( 74) hydrogen bonds : angle 7.17993 / 4.93 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.5416 (OUTLIER) cc_final: 0.5103 (m-30) REVERT: A 95 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 108 LYS cc_start: 0.7392 (tttm) cc_final: 0.6989 (mttm) REVERT: A 121 TRP cc_start: 0.6527 (OUTLIER) cc_final: 0.5823 (m-90) REVERT: A 129 LYS cc_start: 0.5193 (pttt) cc_final: 0.4664 (tttp) REVERT: A 224 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.5778 (m-80) REVERT: A 229 ASP cc_start: 0.5976 (t0) cc_final: 0.5763 (m-30) REVERT: A 230 THR cc_start: 0.4937 (OUTLIER) cc_final: 0.4378 (p) REVERT: A 392 MET cc_start: 0.3977 (tpt) cc_final: 0.3531 (ttp) REVERT: B 39 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.5335 (ptm-80) outliers start: 36 outliers final: 26 residues processed: 94 average time/residue: 0.0669 time to fit residues: 8.1954 Evaluate side-chains 96 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 95 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.204255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.180534 restraints weight = 6683.350| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 2.24 r_work: 0.4240 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 5119 Z= 0.177 Angle : 0.773 9.233 6960 Z= 0.394 Chirality : 0.050 0.258 737 Planarity : 0.007 0.137 898 Dihedral : 8.267 59.249 714 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.64 % Allowed : 19.07 % Favored : 80.29 % Rotamer: Outliers : 6.81 % Allowed : 35.54 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.23 (0.30), residues: 624 helix: -2.49 (0.53), residues: 56 sheet: -2.86 (0.44), residues: 128 loop : -3.05 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 275 TYR 0.046 0.002 TYR A 322 PHE 0.014 0.002 PHE C 53 TRP 0.025 0.002 TRP A 335 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 5117) covalent geometry : angle 0.77310 / 0.39 ( 6956) SS BOND : bond 0.00875 / 0.42 ( 2) SS BOND : angle 0.82747 / 0.43 ( 4) hydrogen bonds : bond 0.03740 / 2.66 ( 74) hydrogen bonds : angle 7.25349 / 4.93 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.5392 (OUTLIER) cc_final: 0.5050 (m-30) REVERT: A 95 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 129 LYS cc_start: 0.5271 (pttt) cc_final: 0.4692 (tttp) REVERT: A 224 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5816 (m-80) REVERT: A 230 THR cc_start: 0.4989 (OUTLIER) cc_final: 0.4414 (p) REVERT: A 392 MET cc_start: 0.4002 (tpt) cc_final: 0.3552 (ttp) REVERT: B 39 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.5270 (ptm-80) outliers start: 37 outliers final: 28 residues processed: 97 average time/residue: 0.0634 time to fit residues: 8.2266 Evaluate side-chains 96 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 95 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 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 = 0.4636 r_free = 0.4636 target = 0.208625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.185240 restraints weight = 6696.873| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.23 r_work: 0.4294 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 5119 Z= 0.146 Angle : 0.743 9.339 6960 Z= 0.380 Chirality : 0.048 0.253 737 Planarity : 0.006 0.138 898 Dihedral : 8.051 56.322 714 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.64 % Allowed : 17.15 % Favored : 82.21 % Rotamer: Outliers : 5.89 % Allowed : 35.91 % Favored : 58.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.18 (0.30), residues: 624 helix: -2.48 (0.52), residues: 56 sheet: -2.74 (0.44), residues: 127 loop : -3.04 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.037 0.002 TYR A 322 PHE 0.013 0.002 PHE A 65 TRP 0.016 0.001 TRP A 335 HIS 0.007 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5117) covalent geometry : angle 0.74291 / 0.38 ( 6956) SS BOND : bond 0.00830 / 0.40 ( 2) SS BOND : angle 0.70362 / 0.34 ( 4) hydrogen bonds : bond 0.03671 / 2.57 ( 74) hydrogen bonds : angle 7.16226 / 4.87 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.5341 (OUTLIER) cc_final: 0.4985 (m-30) REVERT: A 222 MET cc_start: 0.7641 (tmm) cc_final: 0.7325 (tpt) REVERT: A 224 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.5882 (m-80) REVERT: A 230 THR cc_start: 0.4846 (OUTLIER) cc_final: 0.4344 (p) REVERT: A 392 MET cc_start: 0.3854 (tpt) cc_final: 0.3491 (ttp) outliers start: 32 outliers final: 23 residues processed: 91 average time/residue: 0.0652 time to fit residues: 7.9886 Evaluate side-chains 88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 95 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 391 GLN ** B 54 HIS ** 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 = 0.4629 r_free = 0.4629 target = 0.207945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.184496 restraints weight = 6721.640| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 2.22 r_work: 0.4289 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 5119 Z= 0.152 Angle : 0.754 9.109 6960 Z= 0.385 Chirality : 0.049 0.275 737 Planarity : 0.006 0.138 898 Dihedral : 8.081 55.597 714 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.64 % Allowed : 18.27 % Favored : 81.09 % Rotamer: Outliers : 5.16 % Allowed : 36.83 % Favored : 58.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -4.11 (0.30), residues: 624 helix: -2.19 (0.56), residues: 53 sheet: -2.91 (0.42), residues: 137 loop : -2.93 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 275 TYR 0.036 0.002 TYR A 322 PHE 0.024 0.002 PHE A 65 TRP 0.019 0.001 TRP A 335 HIS 0.007 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 5117) covalent geometry : angle 0.75374 / 0.38 ( 6956) SS BOND : bond 0.01042 / 0.50 ( 2) SS BOND : angle 0.82188 / 0.40 ( 4) hydrogen bonds : bond 0.03702 / 2.64 ( 74) hydrogen bonds : angle 7.00009 / 4.80 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1302.92 seconds wall clock time: 23 minutes 15.38 seconds (1395.38 seconds total)