Starting phenix.real_space_refine on Thu Oct 22 17:59:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26qg_80824/10_2026/26qg_80824_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/26qg_80824/10_2026/26qg_80824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26qg_80824/10_2026/26qg_80824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26qg_80824/10_2026/26qg_80824.map" model { file = "/net/cci-nas-00/data/ceres_data/26qg_80824/10_2026/26qg_80824_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26qg_80824/10_2026/26qg_80824_neut.cif" } resolution = 3.2 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= 0.083 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 28 5.16 5 C 2022 2.51 5 N 504 2.21 5 O 539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3095 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3042 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'6CM': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.04, per 1000 atoms: 0.34 Number of scatterers: 3095 At special positions: 0 Unit cell: (62.78, 62.78, 86.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 2 15.00 O 539 8.00 N 504 7.00 C 2022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 323 " 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: 0.32 Conformation dependent library (CDL) restraints added in 116.7 milliseconds 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 61.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 1 through 36 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 92 through 105 removed outlier: 4.242A pdb=" N ASP A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.663A pdb=" N ASN A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 128' Processing helix chain 'A' and resid 128 through 135 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 179 through 204 removed outlier: 5.550A pdb=" N HIS A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix removed outlier: 3.573A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 234 through 247 removed outlier: 3.526A pdb=" N GLY A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 292 through 295 removed outlier: 4.208A pdb=" N GLU A 295 " --> pdb=" O PRO A 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.712A pdb=" N ILE A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 339 Processing helix chain 'A' and resid 345 through 368 removed outlier: 4.399A pdb=" N ILE A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 8.781A pdb=" N ARG A 111 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 83 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 113 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 85 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER A 54 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS A 143 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 56 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS A 213 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER A 212 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 168 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLY A 166 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL A 165 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 11.951A pdb=" N SER A 253 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 12.689A pdb=" N LEU A 167 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 12.577A pdb=" N GLN A 255 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N HIS A 169 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA A 257 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 171 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN A 259 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR A 173 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 373 removed outlier: 4.250A pdb=" N TYR A 380 " --> pdb=" O ILE A 373 " (cutoff:3.500A) 172 hydrogen bonds defined for protein. 507 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: 0.43 Time building geometry restraints manager: 0.35 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: 944 1.34 - 1.46: 524 1.46 - 1.58: 1651 1.58 - 1.69: 11 1.69 - 1.81: 45 Bond restraints: 3175 Sorted by residual: bond pdb=" N1 UDP A 402 " pdb=" C6 UDP A 402 " ideal model delta sigma weight residual 1.375 1.334 0.041 1.00e-02 1.00e+04 1.69e+01 bond pdb=" N3 UDP A 402 " pdb=" C4 UDP A 402 " ideal model delta sigma weight residual 1.383 1.337 0.046 1.20e-02 6.94e+03 1.47e+01 bond pdb=" C13 6CM A 401 " pdb=" C14 6CM A 401 " ideal model delta sigma weight residual 1.524 1.595 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C15 6CM A 401 " pdb=" C16 6CM A 401 " ideal model delta sigma weight residual 1.524 1.593 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C10 6CM A 401 " pdb=" C9 6CM A 401 " ideal model delta sigma weight residual 1.524 1.590 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 3170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 4256 2.88 - 5.76: 37 5.76 - 8.64: 5 8.64 - 11.53: 2 11.53 - 14.41: 3 Bond angle restraints: 4303 Sorted by residual: angle pdb=" O3A UDP A 402 " pdb=" PB UDP A 402 " pdb=" O3B UDP A 402 " ideal model delta sigma weight residual 112.01 102.99 9.02 1.00e+00 1.00e+00 8.13e+01 angle pdb=" C2 UDP A 402 " pdb=" N3 UDP A 402 " pdb=" C4 UDP A 402 " ideal model delta sigma weight residual 126.93 120.67 6.26 1.00e+00 1.00e+00 3.92e+01 angle pdb=" N3 UDP A 402 " pdb=" C4 UDP A 402 " pdb=" C5 UDP A 402 " ideal model delta sigma weight residual 114.70 120.33 -5.63 1.00e+00 1.00e+00 3.17e+01 angle pdb=" N1 UDP A 402 " pdb=" C2 UDP A 402 " pdb=" N3 UDP A 402 " ideal model delta sigma weight residual 114.79 120.12 -5.33 1.00e+00 1.00e+00 2.84e+01 angle pdb=" C16 6CM A 401 " pdb=" C17 6CM A 401 " pdb=" C18 6CM A 401 " ideal model delta sigma weight residual 112.74 127.15 -14.41 3.00e+00 1.11e-01 2.31e+01 ... (remaining 4298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1661 16.95 - 33.91: 169 33.91 - 50.86: 39 50.86 - 67.82: 10 67.82 - 84.77: 3 Dihedral angle restraints: 1882 sinusoidal: 778 harmonic: 1104 Sorted by residual: dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 323 " pdb=" CB CYS A 323 " ideal model delta sinusoidal sigma weight residual -86.00 -1.23 -84.77 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CA ASP A 152 " pdb=" CB ASP A 152 " pdb=" CG ASP A 152 " pdb=" OD1 ASP A 152 " ideal model delta sinusoidal sigma weight residual -30.00 -82.87 52.87 1 2.00e+01 2.50e-03 9.51e+00 dihedral pdb=" CB MET A 316 " pdb=" CG MET A 316 " pdb=" SD MET A 316 " pdb=" CE MET A 316 " ideal model delta sinusoidal sigma weight residual 60.00 118.03 -58.03 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 382 0.047 - 0.093: 81 0.093 - 0.140: 9 0.140 - 0.187: 1 0.187 - 0.233: 1 Chirality restraints: 474 Sorted by residual: chirality pdb=" C3 6CM A 401 " pdb=" C2 6CM A 401 " pdb=" C4 6CM A 401 " pdb=" O3 6CM A 401 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2' UDP A 402 " pdb=" C3' UDP A 402 " pdb=" O2' UDP A 402 " pdb=" C1' UDP A 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.53 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 471 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 6CM A 401 " 0.088 2.00e-02 2.50e+03 2.79e-01 9.75e+02 pdb=" C2 6CM A 401 " -0.333 2.00e-02 2.50e+03 pdb=" C20 6CM A 401 " -0.190 2.00e-02 2.50e+03 pdb=" N2 6CM A 401 " 0.483 2.00e-02 2.50e+03 pdb=" O19 6CM A 401 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 63 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO A 64 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 323 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C CYS A 323 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS A 323 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 324 " -0.010 2.00e-02 2.50e+03 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 884 2.81 - 3.33: 2888 3.33 - 3.85: 5231 3.85 - 4.38: 5984 4.38 - 4.90: 10272 Nonbonded interactions: 25259 Sorted by model distance: nonbonded pdb=" OG SER A 265 " pdb=" OE1 GLN A 268 " model vdw 2.287 3.040 nonbonded pdb=" O ILE A 121 " pdb=" OH TYR A 380 " model vdw 2.302 3.040 nonbonded pdb=" ND2 ASN A 38 " pdb=" O GLY A 336 " model vdw 2.308 3.120 nonbonded pdb=" O ARG A 195 " pdb=" OG SER A 199 " model vdw 2.329 3.040 nonbonded pdb=" NZ LYS A 278 " pdb=" O ASP A 370 " model vdw 2.335 3.120 ... (remaining 25254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.940 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.080 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.005 0.071 3176 Z= 0.293 Angle : 0.797 14.406 4305 Z= 0.467 Chirality : 0.039 0.233 474 Planarity : 0.013 0.279 530 Dihedral : 14.635 81.111 1171 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.41 % Allowed : 6.81 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.41), residues: 377 helix: 0.61 (0.34), residues: 211 sheet: -2.83 (0.82), residues: 26 loop : -1.83 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.005 0.001 TYR A 349 PHE 0.012 0.001 PHE A 19 TRP 0.005 0.000 TRP A 23 HIS 0.002 0.000 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.29 ( 3175) covalent geometry : angle 0.79276 / 0.47 ( 4303) SS BOND : bond 0.01127 / 0.59 ( 1) SS BOND : angle 3.98605 / 2.24 ( 2) hydrogen bonds : bond 0.15534 / 10.43 ( 172) hydrogen bonds : angle 5.54945 / 4.20 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.087 Fit side-chains REVERT: A 36 HIS cc_start: 0.7068 (t70) cc_final: 0.6755 (t70) REVERT: A 111 ARG cc_start: 0.6543 (ptm160) cc_final: 0.6030 (ptt180) REVERT: A 133 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7354 (tm-30) REVERT: A 383 ARG cc_start: 0.4687 (ptt180) cc_final: 0.4175 (mmm160) REVERT: A 389 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7359 (mm-30) outliers start: 11 outliers final: 4 residues processed: 69 average time/residue: 0.0856 time to fit residues: 6.7857 Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 387 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN A 169 HIS A 186 GLN A 270 GLN A 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131461 restraints weight = 3473.609| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.47 r_work: 0.3475 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3176 Z= 0.165 Angle : 0.589 8.058 4305 Z= 0.306 Chirality : 0.043 0.158 474 Planarity : 0.004 0.032 530 Dihedral : 8.637 74.539 478 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.10 % Allowed : 12.07 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.43), residues: 377 helix: 1.20 (0.34), residues: 219 sheet: -1.99 (0.95), residues: 27 loop : -1.50 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.010 0.001 TYR A 349 PHE 0.017 0.002 PHE A 311 TRP 0.014 0.002 TRP A 23 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 3175) covalent geometry : angle 0.58564 / 0.30 ( 4303) SS BOND : bond 0.01667 / 0.88 ( 1) SS BOND : angle 3.02190 / 1.77 ( 2) hydrogen bonds : bond 0.03739 / 2.53 ( 172) hydrogen bonds : angle 4.30652 / 3.09 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.110 Fit side-chains REVERT: A 36 HIS cc_start: 0.7744 (t70) cc_final: 0.7297 (t-90) REVERT: A 111 ARG cc_start: 0.6107 (ptm160) cc_final: 0.5527 (ptt180) REVERT: A 133 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8039 (mt-10) REVERT: A 268 GLN cc_start: 0.7678 (mp10) cc_final: 0.7471 (mt0) REVERT: A 383 ARG cc_start: 0.5838 (ptt180) cc_final: 0.5220 (mmm160) REVERT: A 389 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7274 (mm-30) outliers start: 10 outliers final: 3 residues processed: 66 average time/residue: 0.0573 time to fit residues: 4.5530 Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [19, 26, 25, 34, 3, 28, 9, 35, 8, 13, 37] chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139483 restraints weight = 3435.242| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.03 r_work: 0.3492 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3176 Z= 0.138 Angle : 0.554 8.596 4305 Z= 0.285 Chirality : 0.041 0.158 474 Planarity : 0.004 0.028 530 Dihedral : 7.915 69.641 475 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.41 % Allowed : 14.24 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.44), residues: 377 helix: 1.57 (0.35), residues: 219 sheet: -1.54 (1.02), residues: 27 loop : -1.29 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.009 0.001 TYR A 349 PHE 0.013 0.002 PHE A 327 TRP 0.014 0.001 TRP A 23 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 3175) covalent geometry : angle 0.54994 / 0.28 ( 4303) SS BOND : bond 0.01436 / 0.76 ( 1) SS BOND : angle 3.16400 / 1.85 ( 2) hydrogen bonds : bond 0.03495 / 2.39 ( 172) hydrogen bonds : angle 4.15916 / 3.02 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.160 Fit side-chains REVERT: A 111 ARG cc_start: 0.6339 (ptm160) cc_final: 0.5759 (ptt180) REVERT: A 245 ASP cc_start: 0.7710 (m-30) cc_final: 0.7495 (t0) REVERT: A 268 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: A 383 ARG cc_start: 0.6271 (ptt180) cc_final: 0.5591 (mmm160) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.0687 time to fit residues: 5.5843 Evaluate side-chains 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [30, 35, 15, 27, 13, 6, 21, 11, 18, 28, 12] chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 27 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141012 restraints weight = 3349.612| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.01 r_work: 0.3504 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3176 Z= 0.110 Angle : 0.541 8.688 4305 Z= 0.275 Chirality : 0.040 0.165 474 Planarity : 0.003 0.028 530 Dihedral : 7.640 70.087 475 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.02 % Allowed : 15.48 % Favored : 80.50 % 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 are not related in a simple way. whole: 0.83 (0.44), residues: 377 helix: 1.79 (0.35), residues: 218 sheet: -1.83 (0.89), residues: 37 loop : -0.91 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.010 0.001 TYR A 349 PHE 0.016 0.002 PHE A 311 TRP 0.013 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 3175) covalent geometry : angle 0.53665 / 0.27 ( 4303) SS BOND : bond 0.01288 / 0.68 ( 1) SS BOND : angle 3.23757 / 1.90 ( 2) hydrogen bonds : bond 0.03251 / 2.25 ( 172) hydrogen bonds : angle 4.03492 / 2.94 ( 507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.103 Fit side-chains REVERT: A 36 HIS cc_start: 0.8062 (t-90) cc_final: 0.7734 (t-90) REVERT: A 111 ARG cc_start: 0.6379 (ptm160) cc_final: 0.6029 (ptm160) REVERT: A 245 ASP cc_start: 0.7751 (m-30) cc_final: 0.7519 (t0) REVERT: A 268 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: A 381 ARG cc_start: 0.7778 (tmm-80) cc_final: 0.7538 (ttp-170) REVERT: A 383 ARG cc_start: 0.6109 (ptt180) cc_final: 0.5496 (mmm160) REVERT: A 389 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7671 (mm-30) outliers start: 13 outliers final: 7 residues processed: 71 average time/residue: 0.0669 time to fit residues: 5.7146 Evaluate side-chains 65 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [34, 37, 23, 1, 8, 5, 33, 6, 14, 10, 24] chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.169486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138538 restraints weight = 3419.889| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.05 r_work: 0.3475 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3176 Z= 0.124 Angle : 0.566 9.615 4305 Z= 0.290 Chirality : 0.041 0.168 474 Planarity : 0.003 0.029 530 Dihedral : 7.554 69.902 473 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.33 % Allowed : 17.03 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.45), residues: 377 helix: 1.64 (0.35), residues: 224 sheet: -1.69 (0.92), residues: 37 loop : -0.94 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 216 TYR 0.010 0.001 TYR A 349 PHE 0.016 0.002 PHE A 311 TRP 0.013 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 3175) covalent geometry : angle 0.56024 / 0.29 ( 4303) SS BOND : bond 0.01564 / 0.82 ( 1) SS BOND : angle 3.85553 / 2.23 ( 2) hydrogen bonds : bond 0.03392 / 2.33 ( 172) hydrogen bonds : angle 4.01030 / 2.93 ( 507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.110 Fit side-chains REVERT: A 111 ARG cc_start: 0.6364 (ptm160) cc_final: 0.5970 (ptm160) REVERT: A 245 ASP cc_start: 0.7789 (m-30) cc_final: 0.7543 (t0) REVERT: A 268 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: A 295 GLU cc_start: 0.8131 (mp0) cc_final: 0.7199 (pt0) REVERT: A 381 ARG cc_start: 0.7733 (tmm-80) cc_final: 0.7494 (ttp-170) REVERT: A 383 ARG cc_start: 0.6403 (ptt180) cc_final: 0.5830 (mmm160) REVERT: A 389 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7708 (mm-30) outliers start: 14 outliers final: 6 residues processed: 68 average time/residue: 0.0817 time to fit residues: 6.5427 Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [4, 17, 33, 7, 19, 29, 24, 12, 15, 6, 26] chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.169946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139531 restraints weight = 3403.631| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.00 r_work: 0.3493 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3176 Z= 0.114 Angle : 0.546 9.320 4305 Z= 0.278 Chirality : 0.040 0.168 474 Planarity : 0.003 0.028 530 Dihedral : 7.693 69.724 473 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.02 % Allowed : 17.34 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.44), residues: 377 helix: 1.61 (0.35), residues: 224 sheet: -1.67 (0.91), residues: 37 loop : -0.90 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.010 0.001 TYR A 349 PHE 0.016 0.001 PHE A 311 TRP 0.013 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 3175) covalent geometry : angle 0.53966 / 0.28 ( 4303) SS BOND : bond 0.01459 / 0.77 ( 1) SS BOND : angle 3.76797 / 2.19 ( 2) hydrogen bonds : bond 0.03366 / 2.32 ( 172) hydrogen bonds : angle 3.97512 / 2.93 ( 507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.063 Fit side-chains REVERT: A 245 ASP cc_start: 0.7810 (m-30) cc_final: 0.7523 (t0) REVERT: A 268 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: A 295 GLU cc_start: 0.8136 (mp0) cc_final: 0.7240 (pt0) REVERT: A 359 MET cc_start: 0.8068 (ttp) cc_final: 0.7808 (ttt) REVERT: A 381 ARG cc_start: 0.7702 (tmm-80) cc_final: 0.7460 (ttp-170) REVERT: A 383 ARG cc_start: 0.6255 (ptt180) cc_final: 0.5755 (mmm160) outliers start: 13 outliers final: 7 residues processed: 62 average time/residue: 0.0705 time to fit residues: 5.2229 Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [15, 22, 9, 34, 24, 5, 25, 31, 12, 26, 17] chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138110 restraints weight = 3475.343| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.02 r_work: 0.3475 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3176 Z= 0.122 Angle : 0.587 10.918 4305 Z= 0.298 Chirality : 0.041 0.193 474 Planarity : 0.003 0.029 530 Dihedral : 7.808 69.892 473 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.41 % Allowed : 17.65 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.44), residues: 377 helix: 1.60 (0.35), residues: 224 sheet: -1.58 (0.89), residues: 37 loop : -0.84 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 111 TYR 0.010 0.001 TYR A 349 PHE 0.017 0.002 PHE A 311 TRP 0.013 0.001 TRP A 23 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 3175) covalent geometry : angle 0.57391 / 0.29 ( 4303) SS BOND : bond 0.01691 / 0.89 ( 1) SS BOND : angle 5.73290 / 3.26 ( 2) hydrogen bonds : bond 0.03449 / 2.37 ( 172) hydrogen bonds : angle 3.99218 / 2.94 ( 507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.106 Fit side-chains REVERT: A 245 ASP cc_start: 0.7800 (m-30) cc_final: 0.7505 (t0) REVERT: A 268 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: A 295 GLU cc_start: 0.8113 (mp0) cc_final: 0.7711 (mp0) REVERT: A 381 ARG cc_start: 0.7698 (tmm-80) cc_final: 0.7461 (ttp-170) REVERT: A 383 ARG cc_start: 0.6225 (ptt180) cc_final: 0.5858 (mmm160) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.0681 time to fit residues: 4.8834 Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [20, 32, 35, 17, 4, 36, 5, 9, 33, 10, 22] chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135125 restraints weight = 3528.438| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.09 r_work: 0.3444 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3176 Z= 0.152 Angle : 0.614 11.370 4305 Z= 0.313 Chirality : 0.042 0.208 474 Planarity : 0.004 0.030 530 Dihedral : 8.034 69.240 473 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.41 % Allowed : 17.34 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.44), residues: 377 helix: 1.47 (0.35), residues: 225 sheet: -1.12 (1.06), residues: 27 loop : -1.09 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 111 TYR 0.010 0.001 TYR A 349 PHE 0.019 0.002 PHE A 311 TRP 0.014 0.001 TRP A 23 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 3175) covalent geometry : angle 0.60159 / 0.31 ( 4303) SS BOND : bond 0.01636 / 0.86 ( 1) SS BOND : angle 5.67471 / 3.27 ( 2) hydrogen bonds : bond 0.03672 / 2.51 ( 172) hydrogen bonds : angle 4.10648 / 3.01 ( 507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 245 ASP cc_start: 0.7775 (m-30) cc_final: 0.7433 (t0) REVERT: A 268 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: A 295 GLU cc_start: 0.8102 (mp0) cc_final: 0.7314 (pt0) REVERT: A 383 ARG cc_start: 0.6374 (ptt180) cc_final: 0.6035 (mmp80) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.0698 time to fit residues: 5.3983 Evaluate side-chains 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [33, 22, 31, 6, 13, 19, 12, 28, 32, 2, 17] chunk 33 optimal weight: 0.0040 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137696 restraints weight = 3474.428| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.09 r_work: 0.3472 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3176 Z= 0.115 Angle : 0.592 11.261 4305 Z= 0.298 Chirality : 0.041 0.212 474 Planarity : 0.003 0.030 530 Dihedral : 7.849 69.613 473 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.10 % Allowed : 18.58 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.45), residues: 377 helix: 1.63 (0.35), residues: 224 sheet: -1.54 (0.87), residues: 37 loop : -0.68 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.010 0.001 TYR A 349 PHE 0.017 0.002 PHE A 311 TRP 0.013 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 3175) covalent geometry : angle 0.57935 / 0.29 ( 4303) SS BOND : bond 0.01102 / 0.58 ( 1) SS BOND : angle 5.67671 / 3.26 ( 2) hydrogen bonds : bond 0.03400 / 2.34 ( 172) hydrogen bonds : angle 4.02027 / 2.95 ( 507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.061 Fit side-chains REVERT: A 111 ARG cc_start: 0.6158 (ptm160) cc_final: 0.5946 (ptt180) REVERT: A 211 MET cc_start: 0.7820 (mtp) cc_final: 0.7596 (mtp) REVERT: A 245 ASP cc_start: 0.7776 (m-30) cc_final: 0.7446 (t0) REVERT: A 268 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: A 295 GLU cc_start: 0.8054 (mp0) cc_final: 0.7304 (pt0) REVERT: A 389 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7385 (mm-30) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.0590 time to fit residues: 3.9486 Evaluate side-chains 53 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [27, 3, 11, 31, 33, 14, 1, 35, 37, 7, 6] chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135108 restraints weight = 3415.223| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.04 r_work: 0.3435 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3176 Z= 0.141 Angle : 0.617 11.438 4305 Z= 0.312 Chirality : 0.042 0.219 474 Planarity : 0.004 0.030 530 Dihedral : 7.891 70.201 473 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.48 % Allowed : 19.20 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.45), residues: 377 helix: 1.55 (0.35), residues: 224 sheet: -1.52 (0.83), residues: 38 loop : -0.63 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.010 0.001 TYR A 349 PHE 0.018 0.002 PHE A 311 TRP 0.014 0.001 TRP A 23 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 3175) covalent geometry : angle 0.60596 / 0.31 ( 4303) SS BOND : bond 0.01370 / 0.72 ( 1) SS BOND : angle 5.44188 / 3.14 ( 2) hydrogen bonds : bond 0.03580 / 2.44 ( 172) hydrogen bonds : angle 4.08365 / 2.98 ( 507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.086 Fit side-chains REVERT: A 111 ARG cc_start: 0.6141 (ptm160) cc_final: 0.5922 (ptt180) REVERT: A 245 ASP cc_start: 0.7773 (m-30) cc_final: 0.7427 (t0) REVERT: A 268 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7728 (mt0) REVERT: A 295 GLU cc_start: 0.8054 (mp0) cc_final: 0.7151 (pm20) outliers start: 8 outliers final: 7 residues processed: 58 average time/residue: 0.0590 time to fit residues: 4.1196 Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: [36, 33, 11, 23, 37, 12, 24, 31, 26, 28, 15] chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 0.0670 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.167911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137323 restraints weight = 3401.990| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.06 r_work: 0.3459 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3176 Z= 0.120 Angle : 0.588 11.170 4305 Z= 0.296 Chirality : 0.041 0.204 474 Planarity : 0.003 0.030 530 Dihedral : 7.689 71.030 473 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.17 % Allowed : 19.81 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.45), residues: 377 helix: 1.63 (0.35), residues: 224 sheet: -1.46 (0.84), residues: 37 loop : -0.61 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 272 TYR 0.010 0.001 TYR A 349 PHE 0.017 0.002 PHE A 311 TRP 0.013 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3175) covalent geometry : angle 0.57837 / 0.29 ( 4303) SS BOND : bond 0.01349 / 0.71 ( 1) SS BOND : angle 5.04289 / 2.91 ( 2) hydrogen bonds : bond 0.03399 / 2.33 ( 172) hydrogen bonds : angle 3.99250 / 2.92 ( 507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1051.24 seconds wall clock time: 18 minutes 42.57 seconds (1122.57 seconds total)