Starting phenix.real_space_refine on Tue Aug 4 17:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nep_49329/08_2026/9nep_49329.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nep_49329/08_2026/9nep_49329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nep_49329/08_2026/9nep_49329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nep_49329/08_2026/9nep_49329.map" model { file = "/net/cci-nas-00/data/ceres_data/9nep_49329/08_2026/9nep_49329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nep_49329/08_2026/9nep_49329.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 43 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3074 2.51 5 N 884 2.21 5 O 1077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 5112 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4178 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 17, 'TRANS': 512} Chain breaks: 1 Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 933 Classifications: {'RNA': 44} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 17, 'rna3p_pyr': 17} Link IDs: {'rna2p': 9, 'rna3p': 34} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.43, per 1000 atoms: 0.28 Number of scatterers: 5112 At special positions: 0 Unit cell: (63.756, 84.546, 100.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 43 15.00 Mg 1 11.99 O 1077 8.00 N 884 7.00 C 3074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.34 Conformation dependent library (CDL) restraints added in 93.7 milliseconds 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 61.9% alpha, 6.0% beta 13 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 49 through 68 Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 104 through 119 removed outlier: 4.630A pdb=" N SER A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 140 removed outlier: 3.694A pdb=" N GLU A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 219 through 235 Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.590A pdb=" N GLN A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.895A pdb=" N LEU A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.641A pdb=" N GLN A 383 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 407 Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'A' and resid 525 through 535 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420 removed outlier: 3.748A pdb=" N ALA A 414 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE A 371 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 413 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 373 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 415 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 375 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 372 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 467 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 374 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE A 464 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS A 499 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 466 " --> pdb=" O CYS A 499 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 496 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET A 519 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL A 498 " --> pdb=" O MET A 519 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 0.63 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1209 1.33 - 1.45: 1197 1.45 - 1.57: 2749 1.57 - 1.69: 82 1.69 - 1.81: 53 Bond restraints: 5290 Sorted by residual: bond pdb=" C ILE A 440 " pdb=" N PRO A 441 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.23e+00 bond pdb=" N1 G B 30 " pdb=" C2 G B 30 " ideal model delta sigma weight residual 1.373 1.364 0.009 8.00e-03 1.56e+04 1.30e+00 bond pdb=" C4 C B 18 " pdb=" C5 C B 18 " ideal model delta sigma weight residual 1.425 1.416 0.009 8.00e-03 1.56e+04 1.17e+00 bond pdb=" C4 C B 17 " pdb=" C5 C B 17 " ideal model delta sigma weight residual 1.425 1.417 0.008 8.00e-03 1.56e+04 1.11e+00 bond pdb=" CA ILE A 121 " pdb=" CB ILE A 121 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 1.06e+00 ... (remaining 5285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 7117 1.66 - 3.32: 206 3.32 - 4.98: 13 4.98 - 6.64: 2 6.64 - 8.30: 1 Bond angle restraints: 7339 Sorted by residual: angle pdb=" C1' C B 19 " pdb=" N1 C B 19 " pdb=" C2 C B 19 " ideal model delta sigma weight residual 118.80 123.38 -4.58 1.10e+00 8.26e-01 1.74e+01 angle pdb=" N1 C B 19 " pdb=" C2 C B 19 " pdb=" O2 C B 19 " ideal model delta sigma weight residual 118.90 121.09 -2.19 6.00e-01 2.78e+00 1.33e+01 angle pdb=" O5' G B 51 " pdb=" C5' G B 51 " pdb=" C4' G B 51 " ideal model delta sigma weight residual 109.40 112.15 -2.75 8.00e-01 1.56e+00 1.18e+01 angle pdb=" O5' U B 54 " pdb=" C5' U B 54 " pdb=" C4' U B 54 " ideal model delta sigma weight residual 109.40 112.11 -2.71 8.00e-01 1.56e+00 1.15e+01 angle pdb=" N ILE A 508 " pdb=" CA ILE A 508 " pdb=" C ILE A 508 " ideal model delta sigma weight residual 112.29 109.15 3.14 9.40e-01 1.13e+00 1.12e+01 ... (remaining 7334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 3038 35.82 - 71.64: 218 71.64 - 107.46: 28 107.46 - 143.28: 2 143.28 - 179.10: 1 Dihedral angle restraints: 3287 sinusoidal: 1749 harmonic: 1538 Sorted by residual: dihedral pdb=" O4' U B 54 " pdb=" C1' U B 54 " pdb=" N1 U B 54 " pdb=" C2 U B 54 " ideal model delta sinusoidal sigma weight residual -128.00 51.10 -179.10 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' G B 37 " pdb=" C1' G B 37 " pdb=" N9 G B 37 " pdb=" C4 G B 37 " ideal model delta sinusoidal sigma weight residual -106.00 -165.96 59.96 1 1.70e+01 3.46e-03 1.66e+01 dihedral pdb=" CA PHE A 415 " pdb=" C PHE A 415 " pdb=" N SER A 416 " pdb=" CA SER A 416 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 532 0.030 - 0.060: 205 0.060 - 0.090: 77 0.090 - 0.120: 28 0.120 - 0.149: 33 Chirality restraints: 875 Sorted by residual: chirality pdb=" CG LEU A 449 " pdb=" CB LEU A 449 " pdb=" CD1 LEU A 449 " pdb=" CD2 LEU A 449 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" C2' C B 35 " pdb=" C3' C B 35 " pdb=" O2' C B 35 " pdb=" C1' C B 35 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" C2' G B 36 " pdb=" C3' G B 36 " pdb=" O2' G B 36 " pdb=" C1' G B 36 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 872 not shown) Planarity restraints: 766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 67 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" CG ASP A 67 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP A 67 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 67 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 121 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 122 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 67 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ASP A 67 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP A 67 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 68 " -0.008 2.00e-02 2.50e+03 ... (remaining 763 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 155 2.69 - 3.24: 4806 3.24 - 3.79: 8744 3.79 - 4.35: 12095 4.35 - 4.90: 18778 Nonbonded interactions: 44578 Sorted by model distance: nonbonded pdb=" OG1 THR A 502 " pdb=" OD1 ASN A 504 " model vdw 2.134 3.040 nonbonded pdb=" OG1 THR A 394 " pdb=" O MET A 437 " model vdw 2.196 3.040 nonbonded pdb=" NH2 ARG A 484 " pdb=" OD2 ASP A 510 " model vdw 2.242 3.120 nonbonded pdb=" NE2 GLN A 7 " pdb=" O ALA A 474 " model vdw 2.252 3.120 nonbonded pdb=" O GLY A 40 " pdb=" OG SER A 503 " model vdw 2.268 3.040 ... (remaining 44573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5290 Z= 0.198 Angle : 0.579 8.295 7339 Z= 0.389 Chirality : 0.045 0.149 875 Planarity : 0.004 0.039 766 Dihedral : 21.847 179.103 2289 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.41 % Allowed : 25.60 % Favored : 71.99 % 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: -0.38 (0.35), residues: 526 helix: 0.32 (0.28), residues: 296 sheet: -0.43 (0.72), residues: 40 loop : -0.98 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.011 0.001 TYR A 46 PHE 0.010 0.001 PHE A 464 TRP 0.020 0.001 TRP A 155 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.20 ( 5290) covalent geometry : angle 0.57913 / 0.39 ( 7339) hydrogen bonds : bond 0.22171 / 14.34 ( 250) hydrogen bonds : angle 7.75470 / 5.70 ( 696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.170 Fit side-chains REVERT: A 76 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: A 136 LYS cc_start: 0.7987 (tttt) cc_final: 0.7702 (tttm) REVERT: A 208 GLU cc_start: 0.7786 (mp0) cc_final: 0.7484 (mp0) REVERT: A 329 GLU cc_start: 0.8057 (tp30) cc_final: 0.7785 (tp30) REVERT: A 338 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6993 (mtt180) REVERT: A 370 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6659 (mtp180) REVERT: A 451 MET cc_start: 0.8601 (mpp) cc_final: 0.8307 (mpp) REVERT: A 485 GLU cc_start: 0.7905 (tp30) cc_final: 0.7665 (tm-30) outliers start: 11 outliers final: 5 residues processed: 126 average time/residue: 0.6202 time to fit residues: 80.4617 Evaluate side-chains 130 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 507 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103147 restraints weight = 6377.102| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.09 r_work: 0.3144 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5290 Z= 0.184 Angle : 0.570 7.036 7339 Z= 0.313 Chirality : 0.041 0.133 875 Planarity : 0.004 0.032 766 Dihedral : 21.147 177.867 1272 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.41 % Allowed : 24.29 % Favored : 73.30 % 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: 0.28 (0.36), residues: 526 helix: 1.04 (0.29), residues: 311 sheet: -0.47 (0.73), residues: 40 loop : -1.15 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 255 TYR 0.013 0.002 TYR A 46 PHE 0.013 0.002 PHE A 464 TRP 0.009 0.001 TRP A 206 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 5290) covalent geometry : angle 0.56974 / 0.31 ( 7339) hydrogen bonds : bond 0.05672 / 3.76 ( 250) hydrogen bonds : angle 4.92125 / 3.63 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.171 Fit side-chains REVERT: A 76 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: A 78 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8314 (mtmt) REVERT: A 136 LYS cc_start: 0.7981 (tttt) cc_final: 0.7704 (tttm) REVERT: A 208 GLU cc_start: 0.7668 (mp0) cc_final: 0.7302 (mp0) REVERT: A 256 GLU cc_start: 0.7711 (mp0) cc_final: 0.7454 (mp0) REVERT: A 329 GLU cc_start: 0.8040 (tp30) cc_final: 0.7762 (tp30) REVERT: A 451 MET cc_start: 0.8699 (mpp) cc_final: 0.8467 (mpt) REVERT: A 485 GLU cc_start: 0.7882 (tp30) cc_final: 0.7445 (tp30) REVERT: A 532 ASN cc_start: 0.8765 (m-40) cc_final: 0.8528 (m-40) outliers start: 11 outliers final: 4 residues processed: 129 average time/residue: 0.6282 time to fit residues: 83.4436 Evaluate side-chains 125 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 528 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103214 restraints weight = 6342.390| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.09 r_work: 0.3140 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5290 Z= 0.193 Angle : 0.550 9.608 7339 Z= 0.299 Chirality : 0.040 0.182 875 Planarity : 0.004 0.029 766 Dihedral : 21.139 178.628 1256 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.28 % Allowed : 23.85 % Favored : 72.87 % 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: 0.44 (0.37), residues: 526 helix: 1.24 (0.29), residues: 312 sheet: -0.73 (0.72), residues: 40 loop : -1.14 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.013 0.002 TYR A 46 PHE 0.012 0.001 PHE A 464 TRP 0.010 0.002 TRP A 206 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 5290) covalent geometry : angle 0.54969 / 0.30 ( 7339) hydrogen bonds : bond 0.05445 / 3.65 ( 250) hydrogen bonds : angle 4.70269 / 3.47 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.197 Fit side-chains REVERT: A 76 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: A 78 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8344 (mtmt) REVERT: A 136 LYS cc_start: 0.7976 (tttt) cc_final: 0.7746 (tttp) REVERT: A 208 GLU cc_start: 0.7664 (mp0) cc_final: 0.7313 (mp0) REVERT: A 211 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 256 GLU cc_start: 0.7681 (mp0) cc_final: 0.7453 (mp0) REVERT: A 329 GLU cc_start: 0.8048 (tp30) cc_final: 0.7776 (tp30) REVERT: A 451 MET cc_start: 0.8677 (mpp) cc_final: 0.8450 (mpt) REVERT: A 485 GLU cc_start: 0.7829 (tp30) cc_final: 0.7365 (tp30) REVERT: A 531 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8130 (ttt-90) REVERT: A 532 ASN cc_start: 0.8756 (m-40) cc_final: 0.8521 (m-40) outliers start: 15 outliers final: 7 residues processed: 137 average time/residue: 0.5814 time to fit residues: 82.2072 Evaluate side-chains 133 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 531 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103102 restraints weight = 6330.287| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.08 r_work: 0.3140 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5290 Z= 0.207 Angle : 0.558 10.197 7339 Z= 0.301 Chirality : 0.042 0.254 875 Planarity : 0.004 0.029 766 Dihedral : 21.149 178.942 1256 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.19 % Allowed : 25.16 % Favored : 72.65 % 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: 0.46 (0.37), residues: 526 helix: 1.31 (0.29), residues: 312 sheet: -0.81 (0.71), residues: 40 loop : -1.22 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.013 0.002 TYR A 46 PHE 0.012 0.002 PHE A 464 TRP 0.011 0.002 TRP A 206 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 ( 5290) covalent geometry : angle 0.55812 / 0.30 ( 7339) hydrogen bonds : bond 0.05018 / 3.32 ( 250) hydrogen bonds : angle 4.62168 / 3.41 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.104 Fit side-chains REVERT: A 76 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: A 78 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8356 (mtmt) REVERT: A 136 LYS cc_start: 0.7980 (tttt) cc_final: 0.7757 (tttp) REVERT: A 208 GLU cc_start: 0.7651 (mp0) cc_final: 0.7336 (mp0) REVERT: A 211 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7319 (mm-30) REVERT: A 243 GLU cc_start: 0.7214 (mp0) cc_final: 0.6895 (mp0) REVERT: A 256 GLU cc_start: 0.7682 (mp0) cc_final: 0.7459 (mp0) REVERT: A 329 GLU cc_start: 0.8051 (tp30) cc_final: 0.7799 (tp30) REVERT: A 451 MET cc_start: 0.8672 (mpp) cc_final: 0.8424 (mpt) REVERT: A 485 GLU cc_start: 0.7825 (tp30) cc_final: 0.7360 (tp30) REVERT: A 531 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8117 (ttt-90) REVERT: A 532 ASN cc_start: 0.8771 (m-40) cc_final: 0.8549 (m-40) outliers start: 10 outliers final: 6 residues processed: 132 average time/residue: 0.6096 time to fit residues: 82.8309 Evaluate side-chains 136 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 531 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 35 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103926 restraints weight = 6462.115| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.11 r_work: 0.3157 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5290 Z= 0.150 Angle : 0.516 9.535 7339 Z= 0.282 Chirality : 0.039 0.216 875 Planarity : 0.004 0.028 766 Dihedral : 21.105 178.817 1256 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.19 % Allowed : 25.60 % Favored : 72.21 % 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: 0.65 (0.37), residues: 526 helix: 1.49 (0.30), residues: 311 sheet: -0.77 (0.72), residues: 40 loop : -1.21 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 370 TYR 0.011 0.001 TYR A 46 PHE 0.010 0.001 PHE A 464 TRP 0.012 0.001 TRP A 155 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 5290) covalent geometry : angle 0.51601 / 0.28 ( 7339) hydrogen bonds : bond 0.04454 / 2.95 ( 250) hydrogen bonds : angle 4.45268 / 3.28 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.125 Fit side-chains REVERT: A 72 GLU cc_start: 0.7662 (tt0) cc_final: 0.7459 (tt0) REVERT: A 76 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: A 78 LYS cc_start: 0.8573 (mtpp) cc_final: 0.8331 (mtmt) REVERT: A 136 LYS cc_start: 0.7962 (tttt) cc_final: 0.7741 (tttp) REVERT: A 208 GLU cc_start: 0.7630 (mp0) cc_final: 0.7332 (mp0) REVERT: A 211 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 243 GLU cc_start: 0.7241 (mp0) cc_final: 0.6903 (mp0) REVERT: A 256 GLU cc_start: 0.7667 (mp0) cc_final: 0.7437 (mp0) REVERT: A 275 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7405 (mm-30) REVERT: A 329 GLU cc_start: 0.8050 (tp30) cc_final: 0.7798 (tp30) REVERT: A 451 MET cc_start: 0.8688 (mpp) cc_final: 0.8411 (mpt) REVERT: A 485 GLU cc_start: 0.7833 (tp30) cc_final: 0.7366 (tp30) REVERT: A 532 ASN cc_start: 0.8761 (m-40) cc_final: 0.8547 (m-40) outliers start: 10 outliers final: 6 residues processed: 132 average time/residue: 0.6180 time to fit residues: 84.0118 Evaluate side-chains 134 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 528 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103469 restraints weight = 6487.679| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.11 r_work: 0.3146 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5290 Z= 0.203 Angle : 0.561 11.195 7339 Z= 0.299 Chirality : 0.041 0.246 875 Planarity : 0.004 0.029 766 Dihedral : 21.099 178.980 1256 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.19 % Allowed : 26.04 % Favored : 71.77 % 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: 0.55 (0.37), residues: 526 helix: 1.40 (0.29), residues: 312 sheet: -0.81 (0.72), residues: 40 loop : -1.23 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 63 TYR 0.012 0.002 TYR A 46 PHE 0.012 0.002 PHE A 464 TRP 0.014 0.002 TRP A 155 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 ( 5290) covalent geometry : angle 0.56136 / 0.30 ( 7339) hydrogen bonds : bond 0.04689 / 3.10 ( 250) hydrogen bonds : angle 4.49790 / 3.31 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.107 Fit side-chains REVERT: A 76 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: A 78 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8356 (mtmt) REVERT: A 136 LYS cc_start: 0.7961 (tttt) cc_final: 0.7743 (tttp) REVERT: A 208 GLU cc_start: 0.7637 (mp0) cc_final: 0.7331 (mp0) REVERT: A 211 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7339 (mm-30) REVERT: A 243 GLU cc_start: 0.7245 (mp0) cc_final: 0.6895 (mp0) REVERT: A 256 GLU cc_start: 0.7677 (mp0) cc_final: 0.7453 (mp0) REVERT: A 329 GLU cc_start: 0.8053 (tp30) cc_final: 0.7808 (tp30) REVERT: A 451 MET cc_start: 0.8684 (mpp) cc_final: 0.8420 (mpt) REVERT: A 485 GLU cc_start: 0.7847 (tp30) cc_final: 0.7376 (tp30) REVERT: A 531 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8121 (ttt-90) REVERT: A 532 ASN cc_start: 0.8783 (m-40) cc_final: 0.8556 (m-40) outliers start: 10 outliers final: 5 residues processed: 133 average time/residue: 0.5885 time to fit residues: 80.6542 Evaluate side-chains 133 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 531 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 3 optimal weight: 0.2980 chunk 39 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 4 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104657 restraints weight = 6381.275| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.10 r_work: 0.3164 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5290 Z= 0.131 Angle : 0.514 9.265 7339 Z= 0.279 Chirality : 0.038 0.191 875 Planarity : 0.004 0.028 766 Dihedral : 21.058 178.845 1256 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.19 % Allowed : 26.70 % Favored : 71.12 % 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: 0.66 (0.37), residues: 526 helix: 1.49 (0.29), residues: 315 sheet: -0.79 (0.72), residues: 40 loop : -1.23 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 484 TYR 0.009 0.001 TYR A 46 PHE 0.009 0.001 PHE A 464 TRP 0.016 0.001 TRP A 155 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5290) covalent geometry : angle 0.51369 / 0.28 ( 7339) hydrogen bonds : bond 0.04235 / 2.79 ( 250) hydrogen bonds : angle 4.38586 / 3.23 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.107 Fit side-chains REVERT: A 76 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: A 78 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8335 (mtmt) REVERT: A 136 LYS cc_start: 0.7942 (tttt) cc_final: 0.7729 (tttp) REVERT: A 208 GLU cc_start: 0.7642 (mp0) cc_final: 0.7348 (mp0) REVERT: A 211 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 243 GLU cc_start: 0.7258 (mp0) cc_final: 0.6908 (mp0) REVERT: A 256 GLU cc_start: 0.7651 (mp0) cc_final: 0.7417 (mp0) REVERT: A 275 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 329 GLU cc_start: 0.8050 (tp30) cc_final: 0.7811 (tp30) REVERT: A 451 MET cc_start: 0.8682 (mpp) cc_final: 0.8392 (mpt) REVERT: A 485 GLU cc_start: 0.7832 (tp30) cc_final: 0.7340 (tp30) REVERT: A 531 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7907 (ttt-90) REVERT: A 532 ASN cc_start: 0.8770 (m-40) cc_final: 0.8553 (m-40) outliers start: 10 outliers final: 6 residues processed: 129 average time/residue: 0.6001 time to fit residues: 79.7753 Evaluate side-chains 133 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 531 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.0770 chunk 32 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104327 restraints weight = 6398.770| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.10 r_work: 0.3161 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5290 Z= 0.160 Angle : 0.530 9.318 7339 Z= 0.287 Chirality : 0.039 0.194 875 Planarity : 0.004 0.027 766 Dihedral : 21.043 178.832 1256 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.75 % Allowed : 27.79 % Favored : 70.46 % 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: 0.64 (0.37), residues: 526 helix: 1.45 (0.29), residues: 316 sheet: -0.79 (0.72), residues: 40 loop : -1.19 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 484 TYR 0.010 0.001 TYR A 46 PHE 0.011 0.001 PHE A 464 TRP 0.019 0.002 TRP A 155 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 5290) covalent geometry : angle 0.53026 / 0.29 ( 7339) hydrogen bonds : bond 0.04276 / 2.83 ( 250) hydrogen bonds : angle 4.38078 / 3.22 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.101 Fit side-chains REVERT: A 76 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: A 78 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8346 (mtmt) REVERT: A 136 LYS cc_start: 0.7955 (tttt) cc_final: 0.7738 (tttp) REVERT: A 208 GLU cc_start: 0.7651 (mp0) cc_final: 0.7353 (mp0) REVERT: A 211 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 243 GLU cc_start: 0.7248 (mp0) cc_final: 0.6896 (mp0) REVERT: A 256 GLU cc_start: 0.7655 (mp0) cc_final: 0.7432 (mp0) REVERT: A 329 GLU cc_start: 0.8046 (tp30) cc_final: 0.7804 (tp30) REVERT: A 451 MET cc_start: 0.8687 (mpp) cc_final: 0.8398 (mpt) REVERT: A 485 GLU cc_start: 0.7830 (tp30) cc_final: 0.7326 (tp30) REVERT: A 531 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8058 (ttt-90) REVERT: A 532 ASN cc_start: 0.8778 (m-40) cc_final: 0.8551 (m-40) outliers start: 8 outliers final: 5 residues processed: 127 average time/residue: 0.6000 time to fit residues: 78.5606 Evaluate side-chains 131 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 531 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.104799 restraints weight = 6324.816| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.10 r_work: 0.3165 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5290 Z= 0.150 Angle : 0.532 8.975 7339 Z= 0.287 Chirality : 0.039 0.196 875 Planarity : 0.004 0.033 766 Dihedral : 21.012 178.829 1256 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.75 % Allowed : 27.57 % Favored : 70.68 % 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: 0.67 (0.37), residues: 526 helix: 1.51 (0.29), residues: 315 sheet: -0.78 (0.73), residues: 40 loop : -1.23 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 484 TYR 0.010 0.001 TYR A 46 PHE 0.010 0.001 PHE A 464 TRP 0.024 0.002 TRP A 155 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 5290) covalent geometry : angle 0.53194 / 0.29 ( 7339) hydrogen bonds : bond 0.04157 / 2.73 ( 250) hydrogen bonds : angle 4.35485 / 3.20 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.103 Fit side-chains REVERT: A 76 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: A 78 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8350 (mtmt) REVERT: A 136 LYS cc_start: 0.7964 (tttt) cc_final: 0.7742 (tttp) REVERT: A 208 GLU cc_start: 0.7641 (mp0) cc_final: 0.7358 (mp0) REVERT: A 243 GLU cc_start: 0.7250 (mp0) cc_final: 0.6903 (mp0) REVERT: A 256 GLU cc_start: 0.7658 (mp0) cc_final: 0.7427 (mp0) REVERT: A 329 GLU cc_start: 0.8047 (tp30) cc_final: 0.7807 (tp30) REVERT: A 451 MET cc_start: 0.8682 (mpp) cc_final: 0.8395 (mpt) REVERT: A 485 GLU cc_start: 0.7840 (tp30) cc_final: 0.7338 (tp30) REVERT: A 531 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7981 (ttt-90) REVERT: A 532 ASN cc_start: 0.8777 (m-40) cc_final: 0.8539 (m-40) outliers start: 8 outliers final: 5 residues processed: 129 average time/residue: 0.6429 time to fit residues: 85.4647 Evaluate side-chains 134 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 531 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 20 GLN A 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104374 restraints weight = 6401.852| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.10 r_work: 0.3158 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5290 Z= 0.167 Angle : 0.544 9.381 7339 Z= 0.293 Chirality : 0.040 0.193 875 Planarity : 0.004 0.030 766 Dihedral : 21.010 178.875 1256 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.53 % Allowed : 28.88 % Favored : 69.58 % 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: 0.62 (0.37), residues: 526 helix: 1.43 (0.29), residues: 316 sheet: -0.81 (0.72), residues: 40 loop : -1.20 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 484 TYR 0.010 0.001 TYR A 46 PHE 0.011 0.001 PHE A 464 TRP 0.029 0.002 TRP A 155 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 5290) covalent geometry : angle 0.54377 / 0.29 ( 7339) hydrogen bonds : bond 0.04224 / 2.78 ( 250) hydrogen bonds : angle 4.38569 / 3.22 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.176 Fit side-chains REVERT: A 76 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: A 78 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8357 (mtmt) REVERT: A 136 LYS cc_start: 0.7964 (tttt) cc_final: 0.7743 (tttp) REVERT: A 208 GLU cc_start: 0.7636 (mp0) cc_final: 0.7355 (mp0) REVERT: A 243 GLU cc_start: 0.7259 (mp0) cc_final: 0.6909 (mp0) REVERT: A 256 GLU cc_start: 0.7671 (mp0) cc_final: 0.7441 (mp0) REVERT: A 329 GLU cc_start: 0.8059 (tp30) cc_final: 0.7819 (tp30) REVERT: A 451 MET cc_start: 0.8688 (mpp) cc_final: 0.8399 (mpt) REVERT: A 485 GLU cc_start: 0.7843 (tp30) cc_final: 0.7334 (tp30) REVERT: A 531 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7987 (ttt-90) REVERT: A 532 ASN cc_start: 0.8776 (m-40) cc_final: 0.8537 (m-40) outliers start: 7 outliers final: 5 residues processed: 128 average time/residue: 0.5776 time to fit residues: 76.2515 Evaluate side-chains 132 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 531 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 38 optimal weight: 0.0770 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104186 restraints weight = 6529.272| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.11 r_work: 0.3154 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5290 Z= 0.173 Angle : 0.553 9.402 7339 Z= 0.297 Chirality : 0.040 0.198 875 Planarity : 0.004 0.035 766 Dihedral : 21.003 178.912 1256 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.56 % Favored : 95.25 % Rotamer: Outliers : 1.53 % Allowed : 28.45 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.37), residues: 526 helix: 1.39 (0.29), residues: 316 sheet: -0.79 (0.72), residues: 40 loop : -1.23 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 484 TYR 0.010 0.001 TYR A 46 PHE 0.011 0.001 PHE A 464 TRP 0.029 0.002 TRP A 155 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 5290) covalent geometry : angle 0.55318 / 0.30 ( 7339) hydrogen bonds : bond 0.04271 / 2.81 ( 250) hydrogen bonds : angle 4.40054 / 3.24 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.79 seconds wall clock time: 34 minutes 6.03 seconds (2046.03 seconds total)