Starting phenix.real_space_refine on Tue Aug 4 13:31:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v3x_64759/08_2026/9v3x_64759.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v3x_64759/08_2026/9v3x_64759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v3x_64759/08_2026/9v3x_64759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v3x_64759/08_2026/9v3x_64759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v3x_64759/08_2026/9v3x_64759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v3x_64759/08_2026/9v3x_64759.map" } resolution = 3.4 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= -0.003 sd= 0.049 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 23 5.16 5 C 2224 2.51 5 N 528 2.21 5 O 572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3347 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3326 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'NAG-SER': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.72, per 1000 atoms: 0.22 Number of scatterers: 3347 At special positions: 0 Unit cell: (76.36, 63.91, 71.38, 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 23 16.00 O 572 8.00 N 528 7.00 C 2224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 329 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 174 " Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 122.1 milliseconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN A 502 " Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 75.2% alpha, 0.0% 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 48 through 53 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.034A pdb=" N LEU A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 78 through 109 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.695A pdb=" N VAL A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 4.820A pdb=" N HIS A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 removed outlier: 3.636A pdb=" N VAL A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.757A pdb=" N MET A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 removed outlier: 4.274A pdb=" N LEU A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 removed outlier: 3.849A pdb=" N SER A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 287 through 314 removed outlier: 4.467A pdb=" N ILE A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 312 " --> pdb=" O CYS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.965A pdb=" N ILE A 318 " --> pdb=" O GLY A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.767A pdb=" N LEU A 326 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 365 removed outlier: 3.722A pdb=" N LYS A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Proline residue: A 354 - end of helix removed outlier: 3.718A pdb=" N ILE A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.643A pdb=" N ARG A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 393 removed outlier: 3.564A pdb=" N VAL A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 407 removed outlier: 3.971A pdb=" N ILE A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 430 through 444 removed outlier: 4.015A pdb=" N ILE A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.525A pdb=" N GLU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 555 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: 0.41 Time building geometry restraints manager: 0.23 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: 1007 1.34 - 1.46: 705 1.46 - 1.58: 1686 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3432 Sorted by residual: bond pdb=" C TYR A 258 " pdb=" N PRO A 259 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.39e+00 bond pdb=" C DSN A 502 " pdb=" O DSN A 502 " ideal model delta sigma weight residual 1.231 1.259 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C DSN A 502 " pdb=" OXT DSN A 502 " ideal model delta sigma weight residual 1.231 1.259 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C5 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.27e+00 ... (remaining 3427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 4571 2.22 - 4.44: 84 4.44 - 6.66: 24 6.66 - 8.88: 1 8.88 - 11.10: 1 Bond angle restraints: 4681 Sorted by residual: angle pdb=" N PHE A 267 " pdb=" CA PHE A 267 " pdb=" C PHE A 267 " ideal model delta sigma weight residual 114.75 105.95 8.80 1.26e+00 6.30e-01 4.88e+01 angle pdb=" C ILE A 414 " pdb=" N ILE A 415 " pdb=" CA ILE A 415 " ideal model delta sigma weight residual 120.24 122.57 -2.33 6.30e-01 2.52e+00 1.37e+01 angle pdb=" CA PHE A 267 " pdb=" C PHE A 267 " pdb=" N SER A 268 " ideal model delta sigma weight residual 119.80 114.85 4.95 1.34e+00 5.57e-01 1.36e+01 angle pdb=" CA LEU A 202 " pdb=" CB LEU A 202 " pdb=" CG LEU A 202 " ideal model delta sigma weight residual 116.30 127.40 -11.10 3.50e+00 8.16e-02 1.01e+01 angle pdb=" C ILE A 415 " pdb=" CA ILE A 415 " pdb=" CB ILE A 415 " ideal model delta sigma weight residual 114.35 111.36 2.99 1.06e+00 8.90e-01 7.95e+00 ... (remaining 4676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 1835 16.04 - 32.09: 144 32.09 - 48.13: 35 48.13 - 64.18: 5 64.18 - 80.22: 2 Dihedral angle restraints: 2021 sinusoidal: 790 harmonic: 1231 Sorted by residual: dihedral pdb=" CA GLY A 263 " pdb=" C GLY A 263 " pdb=" N THR A 264 " pdb=" CA THR A 264 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASN A 182 " pdb=" C ASN A 182 " pdb=" N ASN A 183 " pdb=" CA ASN A 183 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA THR A 423 " pdb=" C THR A 423 " pdb=" N PHE A 424 " pdb=" CA PHE A 424 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 2018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 347 0.038 - 0.076: 175 0.076 - 0.114: 39 0.114 - 0.152: 6 0.152 - 0.190: 1 Chirality restraints: 568 Sorted by residual: chirality pdb=" CB ILE A 266 " pdb=" CA ILE A 266 " pdb=" CG1 ILE A 266 " pdb=" CG2 ILE A 266 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 174 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA PRO A 431 " pdb=" N PRO A 431 " pdb=" C PRO A 431 " pdb=" CB PRO A 431 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 565 not shown) Planarity restraints: 572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 415 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 416 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 243 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 244 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 416 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 417 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " -0.020 5.00e-02 4.00e+02 ... (remaining 569 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 603 2.77 - 3.30: 3497 3.30 - 3.83: 5576 3.83 - 4.37: 6650 4.37 - 4.90: 11030 Nonbonded interactions: 27356 Sorted by model distance: nonbonded pdb=" O ASP A 115 " pdb=" OG1 THR A 119 " model vdw 2.232 3.040 nonbonded pdb=" O ALA A 172 " pdb=" OG1 THR A 176 " model vdw 2.247 3.040 nonbonded pdb=" NE2 HIS A 103 " pdb=" OE2 GLU A 279 " model vdw 2.295 3.120 nonbonded pdb=" OE2 GLU A 171 " pdb=" OG1 THR A 191 " model vdw 2.315 3.040 nonbonded pdb=" O LEU A 419 " pdb=" OG1 THR A 423 " model vdw 2.318 3.040 ... (remaining 27351 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.180 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: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.003 0.044 3434 Z= 0.164 Angle : 0.800 11.099 4686 Z= 0.454 Chirality : 0.044 0.190 568 Planarity : 0.005 0.047 571 Dihedral : 12.835 80.222 1226 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.92 (0.40), residues: 422 helix: -0.90 (0.31), residues: 285 sheet: None (None), residues: 0 loop : -1.81 (0.48), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 108 TYR 0.008 0.001 TYR A 332 PHE 0.019 0.002 PHE A 238 TRP 0.011 0.001 TRP A 131 HIS 0.003 0.000 HIS A 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 3432) covalent geometry : angle 0.80039 / 0.45 ( 4681) SS BOND : bond 0.00255 / 0.16 ( 1) SS BOND : angle 0.68457 / 0.31 ( 2) hydrogen bonds : bond 0.17139 / 11.06 ( 192) hydrogen bonds : angle 6.88881 / 4.95 ( 555) link_NAG-ASN : bond 0.00113 / 0.07 ( 1) link_NAG-ASN : angle 0.83821 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.073 Fit side-chains REVERT: A 225 ASN cc_start: 0.8593 (m-40) cc_final: 0.8344 (m-40) REVERT: A 436 LYS cc_start: 0.6154 (tptt) cc_final: 0.5735 (ttpp) REVERT: A 448 PHE cc_start: 0.6642 (t80) cc_final: 0.6442 (t80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0421 time to fit residues: 5.1332 Evaluate side-chains 79 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136163 restraints weight = 4108.035| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.40 r_work: 0.3451 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3434 Z= 0.145 Angle : 0.714 9.043 4686 Z= 0.354 Chirality : 0.044 0.161 568 Planarity : 0.005 0.047 571 Dihedral : 5.494 41.523 475 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.67 % Allowed : 10.16 % Favored : 87.17 % 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: -1.67 (0.40), residues: 422 helix: -0.73 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.72 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.006 0.001 TYR A 197 PHE 0.023 0.001 PHE A 424 TRP 0.012 0.001 TRP A 131 HIS 0.002 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 3432) covalent geometry : angle 0.71346 / 0.35 ( 4681) SS BOND : bond 0.00157 / 0.10 ( 1) SS BOND : angle 0.89819 / 0.43 ( 2) hydrogen bonds : bond 0.04096 / 2.61 ( 192) hydrogen bonds : angle 4.79477 / 3.38 ( 555) link_NAG-ASN : bond 0.00249 / 0.16 ( 1) link_NAG-ASN : angle 0.69466 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.072 Fit side-chains REVERT: A 192 MET cc_start: 0.7155 (ttt) cc_final: 0.6936 (ptt) REVERT: A 225 ASN cc_start: 0.8742 (m-40) cc_final: 0.8428 (m110) REVERT: A 436 LYS cc_start: 0.6076 (tptt) cc_final: 0.5481 (ttpp) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.0464 time to fit residues: 5.4843 Evaluate side-chains 88 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.177374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143213 restraints weight = 4114.338| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.45 r_work: 0.3568 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3434 Z= 0.135 Angle : 0.675 8.451 4686 Z= 0.335 Chirality : 0.043 0.160 568 Planarity : 0.005 0.047 571 Dihedral : 5.321 36.601 475 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.87 % Allowed : 14.17 % Favored : 83.96 % 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: -1.53 (0.40), residues: 422 helix: -0.64 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -1.67 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 108 TYR 0.005 0.001 TYR A 258 PHE 0.020 0.001 PHE A 424 TRP 0.006 0.001 TRP A 131 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 3432) covalent geometry : angle 0.67489 / 0.34 ( 4681) SS BOND : bond 0.00175 / 0.11 ( 1) SS BOND : angle 0.91008 / 0.43 ( 2) hydrogen bonds : bond 0.03737 / 2.38 ( 192) hydrogen bonds : angle 4.51017 / 3.22 ( 555) link_NAG-ASN : bond 0.00184 / 0.11 ( 1) link_NAG-ASN : angle 0.66932 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.101 Fit side-chains REVERT: A 74 ASN cc_start: 0.8062 (m110) cc_final: 0.7807 (m-40) REVERT: A 132 LEU cc_start: 0.8571 (pt) cc_final: 0.8294 (mp) REVERT: A 225 ASN cc_start: 0.8750 (m-40) cc_final: 0.8331 (m110) REVERT: A 436 LYS cc_start: 0.6122 (tptt) cc_final: 0.5501 (ttpp) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.0416 time to fit residues: 4.8426 Evaluate side-chains 91 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140862 restraints weight = 4122.436| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.47 r_work: 0.3547 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3434 Z= 0.146 Angle : 0.678 8.325 4686 Z= 0.335 Chirality : 0.044 0.162 568 Planarity : 0.005 0.049 571 Dihedral : 5.236 36.030 475 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.94 % Allowed : 16.84 % Favored : 80.21 % 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: -1.50 (0.40), residues: 422 helix: -0.65 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 108 TYR 0.006 0.001 TYR A 258 PHE 0.018 0.002 PHE A 424 TRP 0.007 0.001 TRP A 131 HIS 0.001 0.000 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 3432) covalent geometry : angle 0.67797 / 0.34 ( 4681) SS BOND : bond 0.00155 / 0.10 ( 1) SS BOND : angle 0.88175 / 0.42 ( 2) hydrogen bonds : bond 0.03629 / 2.31 ( 192) hydrogen bonds : angle 4.41323 / 3.16 ( 555) link_NAG-ASN : bond 0.00204 / 0.13 ( 1) link_NAG-ASN : angle 0.63157 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.076 Fit side-chains REVERT: A 132 LEU cc_start: 0.8570 (pt) cc_final: 0.8366 (mp) REVERT: A 140 ARG cc_start: 0.7635 (ppt170) cc_final: 0.7334 (ttp80) REVERT: A 192 MET cc_start: 0.7137 (ttt) cc_final: 0.6670 (ptt) REVERT: A 196 LEU cc_start: 0.7728 (mm) cc_final: 0.7399 (mm) REVERT: A 225 ASN cc_start: 0.8731 (m-40) cc_final: 0.8290 (m110) REVERT: A 306 LEU cc_start: 0.8740 (mt) cc_final: 0.8506 (tt) REVERT: A 436 LYS cc_start: 0.6168 (tptt) cc_final: 0.5543 (ttpp) outliers start: 11 outliers final: 7 residues processed: 98 average time/residue: 0.0369 time to fit residues: 4.5515 Evaluate side-chains 93 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.172585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137502 restraints weight = 4136.242| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.47 r_work: 0.3501 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3434 Z= 0.176 Angle : 0.706 8.478 4686 Z= 0.350 Chirality : 0.045 0.165 568 Planarity : 0.005 0.051 571 Dihedral : 5.270 37.969 475 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.21 % Allowed : 19.52 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.39), residues: 422 helix: -0.69 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.51 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.007 0.001 TYR A 258 PHE 0.017 0.002 PHE A 424 TRP 0.005 0.001 TRP A 330 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 3432) covalent geometry : angle 0.70603 / 0.35 ( 4681) SS BOND : bond 0.00122 / 0.08 ( 1) SS BOND : angle 0.81662 / 0.39 ( 2) hydrogen bonds : bond 0.03748 / 2.38 ( 192) hydrogen bonds : angle 4.48610 / 3.22 ( 555) link_NAG-ASN : bond 0.00302 / 0.19 ( 1) link_NAG-ASN : angle 0.61958 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.081 Fit side-chains REVERT: A 52 THR cc_start: 0.8957 (t) cc_final: 0.8684 (m) REVERT: A 132 LEU cc_start: 0.8577 (pt) cc_final: 0.8246 (mp) REVERT: A 140 ARG cc_start: 0.7618 (ppt170) cc_final: 0.7109 (ttp80) REVERT: A 167 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8079 (mmmt) REVERT: A 225 ASN cc_start: 0.8775 (m-40) cc_final: 0.8291 (m110) REVERT: A 237 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8227 (tm-30) REVERT: A 436 LYS cc_start: 0.6152 (tptt) cc_final: 0.5497 (ttpp) outliers start: 12 outliers final: 7 residues processed: 96 average time/residue: 0.0518 time to fit residues: 6.3232 Evaluate side-chains 100 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4076 r_free = 0.4076 target = 0.176500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141601 restraints weight = 4101.803| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.46 r_work: 0.3541 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3434 Z= 0.130 Angle : 0.687 8.836 4686 Z= 0.334 Chirality : 0.043 0.161 568 Planarity : 0.005 0.049 571 Dihedral : 5.203 35.836 475 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.48 % Allowed : 20.32 % Favored : 76.20 % 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: -1.29 (0.40), residues: 422 helix: -0.53 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.38 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 108 TYR 0.006 0.001 TYR A 339 PHE 0.017 0.002 PHE A 361 TRP 0.005 0.001 TRP A 131 HIS 0.001 0.000 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3432) covalent geometry : angle 0.68734 / 0.33 ( 4681) SS BOND : bond 0.00114 / 0.07 ( 1) SS BOND : angle 0.77853 / 0.37 ( 2) hydrogen bonds : bond 0.03530 / 2.26 ( 192) hydrogen bonds : angle 4.38375 / 3.16 ( 555) link_NAG-ASN : bond 0.00144 / 0.09 ( 1) link_NAG-ASN : angle 0.67790 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.121 Fit side-chains REVERT: A 132 LEU cc_start: 0.8590 (pt) cc_final: 0.8248 (mp) REVERT: A 225 ASN cc_start: 0.8763 (m-40) cc_final: 0.8470 (m110) REVERT: A 237 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 436 LYS cc_start: 0.6108 (tptt) cc_final: 0.5492 (ttpp) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.0696 time to fit residues: 8.1880 Evaluate side-chains 94 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4079 r_free = 0.4079 target = 0.176734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141482 restraints weight = 4201.267| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.50 r_work: 0.3536 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3434 Z= 0.132 Angle : 0.678 8.151 4686 Z= 0.337 Chirality : 0.043 0.161 568 Planarity : 0.005 0.047 571 Dihedral : 5.095 33.751 475 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.48 % Allowed : 20.32 % Favored : 76.20 % 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: -1.30 (0.40), residues: 422 helix: -0.56 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -1.33 (0.58), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.005 0.001 TYR A 116 PHE 0.020 0.001 PHE A 361 TRP 0.006 0.001 TRP A 131 HIS 0.001 0.000 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 3432) covalent geometry : angle 0.67821 / 0.34 ( 4681) SS BOND : bond 0.00117 / 0.07 ( 1) SS BOND : angle 0.71023 / 0.34 ( 2) hydrogen bonds : bond 0.03499 / 2.24 ( 192) hydrogen bonds : angle 4.35052 / 3.17 ( 555) link_NAG-ASN : bond 0.00233 / 0.15 ( 1) link_NAG-ASN : angle 0.57145 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.087 Fit side-chains REVERT: A 132 LEU cc_start: 0.8577 (pt) cc_final: 0.8070 (mp) REVERT: A 167 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7827 (mmmt) REVERT: A 225 ASN cc_start: 0.8728 (m-40) cc_final: 0.8452 (m110) REVERT: A 237 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 436 LYS cc_start: 0.6092 (tptt) cc_final: 0.5504 (ttpp) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 0.0508 time to fit residues: 5.7639 Evaluate side-chains 91 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4051 r_free = 0.4051 target = 0.173936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138461 restraints weight = 4246.166| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.53 r_work: 0.3502 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3434 Z= 0.158 Angle : 0.701 8.285 4686 Z= 0.348 Chirality : 0.045 0.165 568 Planarity : 0.005 0.049 571 Dihedral : 5.094 33.541 475 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.67 % Allowed : 22.73 % Favored : 74.60 % 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: -1.35 (0.40), residues: 422 helix: -0.59 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.37 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 108 TYR 0.007 0.001 TYR A 332 PHE 0.019 0.002 PHE A 238 TRP 0.006 0.001 TRP A 131 HIS 0.001 0.000 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 3432) covalent geometry : angle 0.70069 / 0.35 ( 4681) SS BOND : bond 0.00037 / 0.02 ( 1) SS BOND : angle 0.62884 / 0.30 ( 2) hydrogen bonds : bond 0.03630 / 2.29 ( 192) hydrogen bonds : angle 4.41810 / 3.23 ( 555) link_NAG-ASN : bond 0.00218 / 0.14 ( 1) link_NAG-ASN : angle 0.56703 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.120 Fit side-chains REVERT: A 108 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7814 (ttp80) REVERT: A 132 LEU cc_start: 0.8611 (pt) cc_final: 0.8116 (mp) REVERT: A 225 ASN cc_start: 0.8744 (m-40) cc_final: 0.8453 (m110) REVERT: A 241 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7221 (pt0) REVERT: A 436 LYS cc_start: 0.6228 (tptt) cc_final: 0.5543 (ttpp) outliers start: 10 outliers final: 8 residues processed: 94 average time/residue: 0.0423 time to fit residues: 5.0189 Evaluate side-chains 96 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4048 r_free = 0.4048 target = 0.173744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138540 restraints weight = 4193.217| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.49 r_work: 0.3490 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3434 Z= 0.161 Angle : 0.718 8.229 4686 Z= 0.359 Chirality : 0.045 0.164 568 Planarity : 0.005 0.050 571 Dihedral : 5.088 34.146 475 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.67 % Allowed : 21.39 % Favored : 75.94 % 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: -1.36 (0.39), residues: 422 helix: -0.59 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -1.40 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.014 0.001 TYR A 332 PHE 0.018 0.002 PHE A 361 TRP 0.006 0.001 TRP A 131 HIS 0.001 0.000 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 3432) covalent geometry : angle 0.71778 / 0.36 ( 4681) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.87643 / 0.42 ( 2) hydrogen bonds : bond 0.03638 / 2.32 ( 192) hydrogen bonds : angle 4.48331 / 3.28 ( 555) link_NAG-ASN : bond 0.00190 / 0.12 ( 1) link_NAG-ASN : angle 0.61922 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.070 Fit side-chains REVERT: A 108 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7826 (ttp80) REVERT: A 132 LEU cc_start: 0.8635 (pt) cc_final: 0.8110 (mp) REVERT: A 225 ASN cc_start: 0.8744 (m-40) cc_final: 0.8450 (m110) REVERT: A 436 LYS cc_start: 0.6229 (tptt) cc_final: 0.5530 (ttpp) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.0367 time to fit residues: 4.1976 Evaluate side-chains 94 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4073 r_free = 0.4073 target = 0.176137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.140660 restraints weight = 4137.560| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.52 r_work: 0.3526 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3434 Z= 0.140 Angle : 0.697 8.360 4686 Z= 0.346 Chirality : 0.044 0.163 568 Planarity : 0.005 0.049 571 Dihedral : 5.013 33.014 475 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.41 % Allowed : 21.39 % Favored : 76.20 % 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: -1.26 (0.40), residues: 422 helix: -0.52 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.36 (0.59), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.010 0.001 TYR A 332 PHE 0.018 0.002 PHE A 361 TRP 0.005 0.001 TRP A 131 HIS 0.001 0.000 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 3432) covalent geometry : angle 0.69674 / 0.35 ( 4681) SS BOND : bond 0.00046 / 0.03 ( 1) SS BOND : angle 0.79290 / 0.37 ( 2) hydrogen bonds : bond 0.03559 / 2.28 ( 192) hydrogen bonds : angle 4.43851 / 3.25 ( 555) link_NAG-ASN : bond 0.00174 / 0.11 ( 1) link_NAG-ASN : angle 0.60882 / 0.27 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.101 Fit side-chains REVERT: A 108 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7816 (ttp80) REVERT: A 132 LEU cc_start: 0.8624 (pt) cc_final: 0.8102 (mp) REVERT: A 225 ASN cc_start: 0.8713 (m-40) cc_final: 0.8393 (m110) REVERT: A 436 LYS cc_start: 0.6147 (tptt) cc_final: 0.5446 (ttpt) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.0429 time to fit residues: 4.9087 Evaluate side-chains 93 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 424 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 2 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4073 r_free = 0.4073 target = 0.176013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140642 restraints weight = 4228.734| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.55 r_work: 0.3519 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3434 Z= 0.146 Angle : 0.705 8.476 4686 Z= 0.352 Chirality : 0.044 0.164 568 Planarity : 0.005 0.049 571 Dihedral : 4.981 32.103 475 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.41 % Allowed : 21.12 % Favored : 76.47 % 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: -1.23 (0.40), residues: 422 helix: -0.50 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -1.32 (0.59), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.021 0.001 TYR A 332 PHE 0.019 0.002 PHE A 238 TRP 0.005 0.001 TRP A 131 HIS 0.001 0.000 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 3432) covalent geometry : angle 0.70509 / 0.35 ( 4681) SS BOND : bond 0.00045 / 0.03 ( 1) SS BOND : angle 0.73834 / 0.33 ( 2) hydrogen bonds : bond 0.03594 / 2.27 ( 192) hydrogen bonds : angle 4.44280 / 3.26 ( 555) link_NAG-ASN : bond 0.00174 / 0.11 ( 1) link_NAG-ASN : angle 0.58052 / 0.26 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 763.12 seconds wall clock time: 13 minutes 43.83 seconds (823.83 seconds total)