Starting phenix.real_space_refine on Tue Feb 3 20:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h61_51894/02_2026/9h61_51894_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h61_51894/02_2026/9h61_51894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h61_51894/02_2026/9h61_51894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h61_51894/02_2026/9h61_51894.map" model { file = "/net/cci-nas-00/data/ceres_data/9h61_51894/02_2026/9h61_51894_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h61_51894/02_2026/9h61_51894_trim.cif" } resolution = 3.21 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= 0.015 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 S 20 5.16 5 C 2217 2.51 5 N 523 2.21 5 O 551 1.98 5 H 3305 0.53 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6597 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 17, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 1.50, per 1000 atoms: 0.23 Number of scatterers: 6616 At special positions: 0 Unit cell: (78.934, 62.112, 73.758, 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 20 16.00 O 551 8.00 N 523 7.00 C 2217 6.00 H 3305 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 465 " 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 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 281.5 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 85.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.516A pdb=" N TRP A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.654A pdb=" N THR A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.727A pdb=" N GLN A 71 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 108 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.932A pdb=" N ASP A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 161 removed outlier: 3.549A pdb=" N ARG A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 181 Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 188 through 193 removed outlier: 5.080A pdb=" N ILE A 193 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 217 removed outlier: 4.078A pdb=" N GLY A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 249 through 255 removed outlier: 3.700A pdb=" N ILE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 255' Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 262 through 290 removed outlier: 3.630A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.543A pdb=" N THR A 295 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 354 through 368 removed outlier: 3.912A pdb=" N VAL A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 370 through 382 removed outlier: 4.038A pdb=" N ASN A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 388 through 399 removed outlier: 3.636A pdb=" N HIS A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 Processing helix chain 'A' and resid 417 through 436 Processing helix chain 'A' and resid 438 through 457 removed outlier: 3.545A pdb=" N GLN A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 657 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: 1.41 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3299 1.03 - 1.23: 6 1.23 - 1.42: 1511 1.42 - 1.61: 1875 1.61 - 1.81: 32 Bond restraints: 6723 Sorted by residual: bond pdb=" N GLY A 44 " pdb=" CA GLY A 44 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.04e+00 bond pdb=" N GLY A 44 " pdb=" H GLY A 44 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C17 IAC A 500 " pdb=" C18 IAC A 500 " ideal model delta sigma weight residual 1.547 1.521 0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" C3 IAC A 500 " pdb=" C4 IAC A 500 " ideal model delta sigma weight residual 1.405 1.388 0.017 2.00e-02 2.50e+03 6.97e-01 bond pdb=" C THR A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.35e-01 ... (remaining 6718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 11624 1.24 - 2.47: 443 2.47 - 3.71: 26 3.71 - 4.95: 5 4.95 - 6.18: 1 Bond angle restraints: 12099 Sorted by residual: angle pdb=" N VAL A 249 " pdb=" CA VAL A 249 " pdb=" C VAL A 249 " ideal model delta sigma weight residual 111.77 109.01 2.76 1.04e+00 9.25e-01 7.06e+00 angle pdb=" N GLY A 325 " pdb=" CA GLY A 325 " pdb=" C GLY A 325 " ideal model delta sigma weight residual 115.32 112.07 3.25 1.31e+00 5.83e-01 6.17e+00 angle pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" C VAL A 359 " ideal model delta sigma weight residual 112.35 109.53 2.82 1.20e+00 6.94e-01 5.50e+00 angle pdb=" CA PRO A 391 " pdb=" N PRO A 391 " pdb=" CD PRO A 391 " ideal model delta sigma weight residual 112.00 108.82 3.18 1.40e+00 5.10e-01 5.15e+00 angle pdb=" N ALA A 59 " pdb=" CA ALA A 59 " pdb=" C ALA A 59 " ideal model delta sigma weight residual 112.72 109.89 2.83 1.28e+00 6.10e-01 4.89e+00 ... (remaining 12094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 2887 17.06 - 34.12: 195 34.12 - 51.17: 73 51.17 - 68.23: 27 68.23 - 85.29: 9 Dihedral angle restraints: 3191 sinusoidal: 1624 harmonic: 1567 Sorted by residual: dihedral pdb=" CB CYS A 462 " pdb=" SG CYS A 462 " pdb=" SG CYS A 465 " pdb=" CB CYS A 465 " ideal model delta sinusoidal sigma weight residual 93.00 174.40 -81.40 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB MET A 446 " pdb=" CG MET A 446 " pdb=" SD MET A 446 " pdb=" CE MET A 446 " ideal model delta sinusoidal sigma weight residual 60.00 116.44 -56.44 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA MET A 257 " pdb=" C MET A 257 " pdb=" N TRP A 258 " pdb=" CA TRP A 258 " ideal model delta harmonic sigma weight residual 180.00 164.94 15.06 0 5.00e+00 4.00e-02 9.07e+00 ... (remaining 3188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 324 0.025 - 0.049: 119 0.049 - 0.074: 63 0.074 - 0.099: 13 0.099 - 0.123: 4 Chirality restraints: 523 Sorted by residual: chirality pdb=" CA ILE A 185 " pdb=" N ILE A 185 " pdb=" C ILE A 185 " pdb=" CB ILE A 185 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE A 118 " pdb=" N ILE A 118 " pdb=" C ILE A 118 " pdb=" CB ILE A 118 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" C PRO A 373 " pdb=" CB PRO A 373 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 520 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 390 " -0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO A 391 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 355 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.52e+00 pdb=" N PRO A 356 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 359 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 360 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.021 5.00e-02 4.00e+02 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 1134 2.29 - 2.87: 15219 2.87 - 3.44: 17975 3.44 - 4.02: 24592 4.02 - 4.60: 37496 Nonbonded interactions: 96416 Sorted by model distance: nonbonded pdb=" O LEU A 279 " pdb=" HG SER A 283 " model vdw 1.709 2.450 nonbonded pdb=" OD1 ASP A 167 " pdb=" H THR A 170 " model vdw 1.709 2.450 nonbonded pdb=" O TYR A 161 " pdb="HH21 ARG A 309 " model vdw 1.732 2.450 nonbonded pdb=" O LEU A 199 " pdb=" HG1 THR A 203 " model vdw 1.760 2.450 nonbonded pdb=" HG SER A 206 " pdb=" O LEU A 277 " model vdw 1.777 2.450 ... (remaining 96411 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: 3.390 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: 0.040 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3419 Z= 0.119 Angle : 0.510 6.184 4665 Z= 0.301 Chirality : 0.033 0.123 523 Planarity : 0.005 0.085 562 Dihedral : 13.049 76.162 1147 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 0.45 (0.44), residues: 406 helix: 0.51 (0.30), residues: 308 sheet: None (None), residues: 0 loop : 0.01 (0.73), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 411 TYR 0.005 0.001 TYR A 161 PHE 0.012 0.001 PHE A 69 TRP 0.009 0.001 TRP A 362 HIS 0.001 0.000 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 3418) covalent geometry : angle 0.50923 ( 4663) SS BOND : bond 0.00283 ( 1) SS BOND : angle 0.95445 ( 2) hydrogen bonds : bond 0.23249 ( 226) hydrogen bonds : angle 8.99499 ( 657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7758 (mtmt) REVERT: A 352 MET cc_start: 0.6757 (tmm) cc_final: 0.6496 (tmm) REVERT: A 420 MET cc_start: 0.7565 (tmm) cc_final: 0.7266 (tpp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1576 time to fit residues: 11.6968 Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 151 GLN A 375 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130050 restraints weight = 11097.064| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.10 r_work: 0.3395 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3419 Z= 0.164 Angle : 0.528 5.633 4665 Z= 0.293 Chirality : 0.036 0.127 523 Planarity : 0.006 0.081 562 Dihedral : 5.814 80.810 445 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.29 % Allowed : 4.29 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.42), residues: 406 helix: 0.78 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -0.23 (0.69), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 411 TYR 0.013 0.001 TYR A 208 PHE 0.014 0.001 PHE A 196 TRP 0.006 0.001 TRP A 335 HIS 0.002 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3418) covalent geometry : angle 0.52757 ( 4663) SS BOND : bond 0.00290 ( 1) SS BOND : angle 0.80491 ( 2) hydrogen bonds : bond 0.05867 ( 226) hydrogen bonds : angle 5.97207 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.7166 (tmm) cc_final: 0.6788 (tpp) REVERT: A 453 ILE cc_start: 0.7749 (mm) cc_final: 0.7335 (mm) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.1222 time to fit residues: 9.6523 Evaluate side-chains 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 34 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128720 restraints weight = 11222.789| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.25 r_work: 0.3370 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3419 Z= 0.153 Angle : 0.519 5.837 4665 Z= 0.283 Chirality : 0.035 0.127 523 Planarity : 0.005 0.071 562 Dihedral : 5.834 81.007 445 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 7.14 % Favored : 92.29 % 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: 0.73 (0.42), residues: 406 helix: 0.81 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -0.29 (0.69), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 414 TYR 0.010 0.001 TYR A 67 PHE 0.011 0.001 PHE A 69 TRP 0.006 0.001 TRP A 335 HIS 0.002 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3418) covalent geometry : angle 0.51883 ( 4663) SS BOND : bond 0.00261 ( 1) SS BOND : angle 1.27415 ( 2) hydrogen bonds : bond 0.04963 ( 226) hydrogen bonds : angle 5.46717 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8284 (t80) cc_final: 0.8062 (t80) REVERT: A 336 GLU cc_start: 0.6038 (pt0) cc_final: 0.5827 (pt0) REVERT: A 420 MET cc_start: 0.7195 (tmm) cc_final: 0.6819 (tpp) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.1335 time to fit residues: 9.0979 Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 271 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126379 restraints weight = 11232.051| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.23 r_work: 0.3352 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3419 Z= 0.179 Angle : 0.517 5.583 4665 Z= 0.282 Chirality : 0.036 0.127 523 Planarity : 0.006 0.067 562 Dihedral : 5.984 84.912 445 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.57 % Allowed : 7.43 % Favored : 92.00 % 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: 0.82 (0.42), residues: 406 helix: 0.94 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -0.46 (0.67), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 411 TYR 0.011 0.001 TYR A 204 PHE 0.016 0.002 PHE A 196 TRP 0.008 0.001 TRP A 362 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 3418) covalent geometry : angle 0.51632 ( 4663) SS BOND : bond 0.00060 ( 1) SS BOND : angle 1.15351 ( 2) hydrogen bonds : bond 0.04544 ( 226) hydrogen bonds : angle 5.30066 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8325 (t80) cc_final: 0.8030 (t80) REVERT: A 305 LYS cc_start: 0.8295 (tptp) cc_final: 0.7994 (tptp) REVERT: A 420 MET cc_start: 0.7248 (tmm) cc_final: 0.6986 (tpp) outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.1240 time to fit residues: 8.7848 Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 271 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 18 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129253 restraints weight = 11284.891| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.28 r_work: 0.3376 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3419 Z= 0.124 Angle : 0.481 5.761 4665 Z= 0.262 Chirality : 0.034 0.129 523 Planarity : 0.005 0.062 562 Dihedral : 5.899 84.874 445 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 8.29 % Favored : 91.14 % 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: 1.08 (0.43), residues: 406 helix: 1.13 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -0.37 (0.69), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 411 TYR 0.009 0.001 TYR A 204 PHE 0.010 0.001 PHE A 83 TRP 0.006 0.001 TRP A 362 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3418) covalent geometry : angle 0.48084 ( 4663) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.74446 ( 2) hydrogen bonds : bond 0.04271 ( 226) hydrogen bonds : angle 5.13605 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8292 (t80) cc_final: 0.7894 (t80) REVERT: A 305 LYS cc_start: 0.8254 (tptp) cc_final: 0.8040 (tptp) REVERT: A 420 MET cc_start: 0.7143 (tmm) cc_final: 0.6879 (tpp) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.1162 time to fit residues: 7.9247 Evaluate side-chains 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 115 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127243 restraints weight = 11247.557| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.23 r_work: 0.3350 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3419 Z= 0.169 Angle : 0.516 5.680 4665 Z= 0.281 Chirality : 0.036 0.122 523 Planarity : 0.005 0.061 562 Dihedral : 6.042 85.952 445 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.86 % Allowed : 9.14 % Favored : 90.00 % 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: 0.99 (0.42), residues: 406 helix: 1.07 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -0.45 (0.68), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 411 TYR 0.009 0.001 TYR A 204 PHE 0.016 0.001 PHE A 196 TRP 0.004 0.001 TRP A 362 HIS 0.010 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3418) covalent geometry : angle 0.51569 ( 4663) SS BOND : bond 0.00285 ( 1) SS BOND : angle 0.68039 ( 2) hydrogen bonds : bond 0.04342 ( 226) hydrogen bonds : angle 5.15607 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8337 (t80) cc_final: 0.7922 (t80) REVERT: A 305 LYS cc_start: 0.8282 (tptp) cc_final: 0.7929 (tptp) REVERT: A 420 MET cc_start: 0.7211 (tmm) cc_final: 0.6931 (tpp) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.0892 time to fit residues: 6.3093 Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 271 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.0000 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128401 restraints weight = 11082.043| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.22 r_work: 0.3368 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3419 Z= 0.139 Angle : 0.483 5.862 4665 Z= 0.263 Chirality : 0.035 0.131 523 Planarity : 0.005 0.059 562 Dihedral : 5.964 86.885 445 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.29 % Allowed : 9.43 % Favored : 90.29 % 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: 1.18 (0.43), residues: 406 helix: 1.17 (0.30), residues: 308 sheet: None (None), residues: 0 loop : -0.25 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 411 TYR 0.009 0.001 TYR A 204 PHE 0.010 0.001 PHE A 83 TRP 0.006 0.001 TRP A 362 HIS 0.002 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3418) covalent geometry : angle 0.48255 ( 4663) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.51590 ( 2) hydrogen bonds : bond 0.04157 ( 226) hydrogen bonds : angle 5.06157 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8302 (tptp) cc_final: 0.7952 (tptp) REVERT: A 420 MET cc_start: 0.7111 (tmm) cc_final: 0.6811 (tpp) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.1160 time to fit residues: 7.6030 Evaluate side-chains 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126662 restraints weight = 11264.256| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.22 r_work: 0.3348 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3419 Z= 0.171 Angle : 0.503 5.660 4665 Z= 0.275 Chirality : 0.036 0.124 523 Planarity : 0.006 0.059 562 Dihedral : 6.070 88.906 445 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.86 % Allowed : 8.86 % Favored : 90.29 % 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: 0.94 (0.42), residues: 406 helix: 1.03 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -0.53 (0.70), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 411 TYR 0.010 0.001 TYR A 204 PHE 0.018 0.001 PHE A 196 TRP 0.006 0.001 TRP A 362 HIS 0.002 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 3418) covalent geometry : angle 0.50303 ( 4663) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.61084 ( 2) hydrogen bonds : bond 0.04281 ( 226) hydrogen bonds : angle 5.09037 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.7170 (tmm) cc_final: 0.6848 (tpp) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.1247 time to fit residues: 8.4762 Evaluate side-chains 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 271 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.0270 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.159225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130559 restraints weight = 11149.428| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.19 r_work: 0.3375 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3419 Z= 0.117 Angle : 0.479 5.835 4665 Z= 0.259 Chirality : 0.034 0.125 523 Planarity : 0.005 0.058 562 Dihedral : 6.055 88.967 445 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.57 % Allowed : 9.14 % Favored : 90.29 % 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: 1.08 (0.43), residues: 406 helix: 1.14 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.50 (0.70), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 411 TYR 0.009 0.001 TYR A 204 PHE 0.010 0.001 PHE A 83 TRP 0.007 0.001 TRP A 362 HIS 0.011 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3418) covalent geometry : angle 0.47925 ( 4663) SS BOND : bond 0.00179 ( 1) SS BOND : angle 0.48747 ( 2) hydrogen bonds : bond 0.04064 ( 226) hydrogen bonds : angle 4.99604 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ASN cc_start: 0.6084 (OUTLIER) cc_final: 0.5764 (p0) REVERT: A 352 MET cc_start: 0.6748 (tmm) cc_final: 0.6534 (tmm) REVERT: A 420 MET cc_start: 0.7120 (tmm) cc_final: 0.6792 (tpp) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1153 time to fit residues: 7.7260 Evaluate side-chains 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 115 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128692 restraints weight = 11248.371| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.25 r_work: 0.3378 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3419 Z= 0.136 Angle : 0.492 5.793 4665 Z= 0.264 Chirality : 0.035 0.128 523 Planarity : 0.005 0.058 562 Dihedral : 6.036 89.102 445 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.57 % Allowed : 9.14 % Favored : 90.29 % 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: 1.06 (0.43), residues: 406 helix: 1.12 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.53 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 411 TYR 0.009 0.001 TYR A 204 PHE 0.020 0.001 PHE A 196 TRP 0.005 0.001 TRP A 362 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3418) covalent geometry : angle 0.49165 ( 4663) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.47265 ( 2) hydrogen bonds : bond 0.04064 ( 226) hydrogen bonds : angle 4.99433 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.6761 (tmm) cc_final: 0.6550 (tmm) REVERT: A 420 MET cc_start: 0.7108 (tmm) cc_final: 0.6776 (tpp) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.1299 time to fit residues: 8.0569 Evaluate side-chains 48 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.158430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129136 restraints weight = 11064.897| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.24 r_work: 0.3380 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3419 Z= 0.131 Angle : 0.485 5.845 4665 Z= 0.262 Chirality : 0.035 0.125 523 Planarity : 0.005 0.057 562 Dihedral : 6.009 89.468 445 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.29 % Allowed : 9.71 % Favored : 90.00 % 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: 1.07 (0.43), residues: 406 helix: 1.14 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.56 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 411 TYR 0.009 0.001 TYR A 204 PHE 0.011 0.001 PHE A 83 TRP 0.005 0.001 TRP A 362 HIS 0.002 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3418) covalent geometry : angle 0.48480 ( 4663) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.48933 ( 2) hydrogen bonds : bond 0.04023 ( 226) hydrogen bonds : angle 4.96921 ( 657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.60 seconds wall clock time: 38 minutes 35.96 seconds (2315.96 seconds total)