Starting phenix.real_space_refine on Fri Aug 22 16:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ej5_28176/08_2025/8ej5_28176.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ej5_28176/08_2025/8ej5_28176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ej5_28176/08_2025/8ej5_28176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ej5_28176/08_2025/8ej5_28176.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ej5_28176/08_2025/8ej5_28176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ej5_28176/08_2025/8ej5_28176.map" } resolution = 4.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 3712 2.51 5 N 981 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5818 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3556 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 1.58, per 1000 atoms: 0.27 Number of scatterers: 5818 At special positions: 0 Unit cell: (74.368, 95.616, 131.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 1108 8.00 N 981 7.00 C 3712 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: 0.29 Conformation dependent library (CDL) restraints added in 138.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 59.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 22 through 30 removed outlier: 4.300A pdb=" N GLY A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 60 through 72 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.151A pdb=" N TRP A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.513A pdb=" N LEU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 353 through 367 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.662A pdb=" N VAL A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'B' and resid 2 through 21 removed outlier: 3.824A pdb=" N GLN B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 45 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.529A pdb=" N TYR B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 86 Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.825A pdb=" N GLN C 21 " --> pdb=" O ASN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.526A pdb=" N TYR C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'D' and resid 2 through 21 removed outlier: 3.806A pdb=" N GLN D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 45 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 61 through 68 removed outlier: 3.527A pdb=" N TYR D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 255 removed outlier: 6.199A pdb=" N THR A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 317 removed outlier: 5.139A pdb=" N GLY A 315 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 454 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 434 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 422 " --> pdb=" O PHE A 404 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1171 1.32 - 1.45: 1552 1.45 - 1.57: 3214 1.57 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5966 Sorted by residual: bond pdb=" N VAL A 394 " pdb=" CA VAL A 394 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N VAL A 440 " pdb=" CA VAL A 440 " ideal model delta sigma weight residual 1.462 1.492 -0.031 8.70e-03 1.32e+04 1.23e+01 bond pdb=" N VAL A 425 " pdb=" CA VAL A 425 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.22e+01 bond pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N GLU D 47 " pdb=" CA GLU D 47 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.07e+01 ... (remaining 5961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 6245 1.82 - 3.65: 1697 3.65 - 5.47: 133 5.47 - 7.29: 23 7.29 - 9.12: 2 Bond angle restraints: 8100 Sorted by residual: angle pdb=" CA GLY A 314 " pdb=" C GLY A 314 " pdb=" N GLY A 315 " ideal model delta sigma weight residual 115.11 120.97 -5.86 9.50e-01 1.11e+00 3.81e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 110.56 118.63 -8.07 1.36e+00 5.41e-01 3.52e+01 angle pdb=" N ASN A 284 " pdb=" CA ASN A 284 " pdb=" C ASN A 284 " ideal model delta sigma weight residual 111.54 104.26 7.28 1.36e+00 5.41e-01 2.87e+01 angle pdb=" N LYS A 272 " pdb=" CA LYS A 272 " pdb=" C LYS A 272 " ideal model delta sigma weight residual 111.28 105.48 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" CA LYS A 242 " pdb=" C LYS A 242 " pdb=" O LYS A 242 " ideal model delta sigma weight residual 120.63 114.92 5.71 1.08e+00 8.57e-01 2.80e+01 ... (remaining 8095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3161 16.49 - 32.97: 214 32.97 - 49.46: 63 49.46 - 65.95: 11 65.95 - 82.44: 3 Dihedral angle restraints: 3452 sinusoidal: 1360 harmonic: 2092 Sorted by residual: dihedral pdb=" C ASN A 316 " pdb=" N ASN A 316 " pdb=" CA ASN A 316 " pdb=" CB ASN A 316 " ideal model delta harmonic sigma weight residual -122.60 -133.15 10.55 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" N ASN A 465 " pdb=" CA ASN A 465 " pdb=" CB ASN A 465 " pdb=" CG ASN A 465 " ideal model delta sinusoidal sigma weight residual -180.00 -125.56 -54.44 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ILE A 275 " pdb=" CB ILE A 275 " pdb=" CG1 ILE A 275 " pdb=" CD1 ILE A 275 " ideal model delta sinusoidal sigma weight residual -180.00 -127.13 -52.87 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 3449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 366 0.067 - 0.135: 376 0.135 - 0.202: 85 0.202 - 0.270: 6 0.270 - 0.337: 2 Chirality restraints: 835 Sorted by residual: chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASN A 316 " pdb=" N ASN A 316 " pdb=" C ASN A 316 " pdb=" CB ASN A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 832 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 84 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SER A 84 " 0.064 2.00e-02 2.50e+03 pdb=" O SER A 84 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO A 85 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 78 " 0.045 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR D 78 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR D 78 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR D 78 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR D 78 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 78 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 78 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " 0.042 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR B 78 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " 0.019 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 2740 2.96 - 3.44: 6379 3.44 - 3.93: 10549 3.93 - 4.41: 11549 4.41 - 4.90: 18520 Nonbonded interactions: 49737 Sorted by model distance: nonbonded pdb=" O SER A 84 " pdb=" OE1 GLU B 58 " model vdw 2.472 3.040 nonbonded pdb=" O ARG A 311 " pdb=" N ASP A 456 " model vdw 2.478 3.120 nonbonded pdb=" N PHE A 244 " pdb=" O ILE A 251 " model vdw 2.487 3.120 nonbonded pdb=" O GLY A 281 " pdb=" OD1 ASP A 464 " model vdw 2.488 3.040 nonbonded pdb=" N THR A 318 " pdb=" OD1 ASN A 321 " model vdw 2.490 3.120 ... (remaining 49732 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.740 Find NCS groups from input model: 0.040 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: 9.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 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 : 0.012 0.047 5966 Z= 0.905 Angle : 1.519 9.118 8100 Z= 1.153 Chirality : 0.090 0.337 835 Planarity : 0.010 0.109 1071 Dihedral : 12.691 82.437 2124 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.84 % Allowed : 1.95 % Favored : 97.21 % Rotamer: Outliers : 3.27 % Allowed : 4.91 % Favored : 91.82 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.40 (0.30), residues: 717 helix: 1.44 (0.25), residues: 397 sheet: 0.11 (0.71), residues: 42 loop : 0.49 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 382 TYR 0.045 0.005 TYR D 78 PHE 0.024 0.004 PHE B 77 TRP 0.027 0.006 TRP A 79 HIS 0.019 0.004 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.01199 ( 5966) covalent geometry : angle 1.51889 ( 8100) hydrogen bonds : bond 0.16173 ( 309) hydrogen bonds : angle 7.63068 ( 906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 328 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7439 (ttm) cc_final: 0.6453 (ttm) REVERT: A 33 ILE cc_start: 0.6295 (mt) cc_final: 0.6059 (mt) REVERT: A 74 ASN cc_start: 0.6556 (t0) cc_final: 0.4873 (t0) REVERT: A 80 LEU cc_start: 0.8388 (tp) cc_final: 0.8181 (tp) REVERT: A 176 ASN cc_start: 0.9194 (t0) cc_final: 0.8478 (p0) REVERT: A 179 LEU cc_start: 0.8689 (tp) cc_final: 0.7989 (tp) REVERT: A 229 ASP cc_start: 0.8564 (m-30) cc_final: 0.8296 (m-30) REVERT: A 234 ASP cc_start: 0.8173 (m-30) cc_final: 0.7842 (t0) REVERT: A 241 ASP cc_start: 0.8580 (m-30) cc_final: 0.8082 (p0) REVERT: A 322 LEU cc_start: 0.8657 (tp) cc_final: 0.8281 (tp) REVERT: A 335 PHE cc_start: 0.7934 (t80) cc_final: 0.7420 (t80) REVERT: A 350 ASP cc_start: 0.8412 (m-30) cc_final: 0.7843 (m-30) REVERT: A 357 LEU cc_start: 0.9093 (tp) cc_final: 0.8798 (tp) REVERT: A 361 TYR cc_start: 0.8506 (t80) cc_final: 0.8182 (t80) REVERT: A 362 MET cc_start: 0.9093 (mmm) cc_final: 0.8638 (mmt) REVERT: A 363 HIS cc_start: 0.8420 (t-170) cc_final: 0.8072 (t70) REVERT: A 366 TRP cc_start: 0.7592 (m100) cc_final: 0.7165 (m100) REVERT: A 412 GLN cc_start: 0.8505 (mt0) cc_final: 0.8260 (mt0) REVERT: A 438 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6783 (m-10) REVERT: A 439 ASN cc_start: 0.8977 (t0) cc_final: 0.8442 (t0) REVERT: A 455 ILE cc_start: 0.8795 (mm) cc_final: 0.8249 (mp) REVERT: A 469 PHE cc_start: 0.8974 (p90) cc_final: 0.8695 (p90) REVERT: B 19 LEU cc_start: 0.8990 (mt) cc_final: 0.8728 (mt) REVERT: B 89 ILE cc_start: 0.5995 (pt) cc_final: 0.5415 (pt) REVERT: C 12 MET cc_start: 0.8845 (tpt) cc_final: 0.8053 (tpt) REVERT: C 19 LEU cc_start: 0.9480 (mt) cc_final: 0.9270 (mt) REVERT: C 36 VAL cc_start: 0.9385 (t) cc_final: 0.9032 (m) REVERT: C 38 CYS cc_start: 0.9134 (m) cc_final: 0.7947 (t) REVERT: C 42 LEU cc_start: 0.8909 (mt) cc_final: 0.6001 (mt) REVERT: C 62 LEU cc_start: 0.9434 (tp) cc_final: 0.9090 (tp) REVERT: C 77 PHE cc_start: 0.8051 (t80) cc_final: 0.7832 (t80) REVERT: C 82 TYR cc_start: 0.8394 (t80) cc_final: 0.7898 (t80) REVERT: D 15 LEU cc_start: 0.9449 (tp) cc_final: 0.9114 (tp) REVERT: D 17 ASN cc_start: 0.8021 (m-40) cc_final: 0.7456 (m110) REVERT: D 19 LEU cc_start: 0.9459 (mt) cc_final: 0.9172 (mt) REVERT: D 66 LEU cc_start: 0.8729 (mt) cc_final: 0.8485 (mt) REVERT: D 74 GLN cc_start: 0.8940 (mt0) cc_final: 0.8290 (mm-40) outliers start: 20 outliers final: 5 residues processed: 333 average time/residue: 0.0787 time to fit residues: 33.4836 Evaluate side-chains 197 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS C 20 GLN C 32 ASN D 32 ASN D 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.099811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078473 restraints weight = 24381.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081122 restraints weight = 14810.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082934 restraints weight = 10082.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084207 restraints weight = 7476.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085041 restraints weight = 5924.895| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5966 Z= 0.146 Angle : 0.648 9.685 8100 Z= 0.344 Chirality : 0.044 0.254 835 Planarity : 0.006 0.140 1071 Dihedral : 5.760 88.475 784 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.81 % Favored : 97.91 % Rotamer: Outliers : 0.16 % Allowed : 2.13 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.70 (0.32), residues: 717 helix: 1.82 (0.26), residues: 403 sheet: 0.45 (0.75), residues: 44 loop : 0.29 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 382 TYR 0.019 0.002 TYR D 78 PHE 0.024 0.003 PHE D 25 TRP 0.037 0.002 TRP A 156 HIS 0.003 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5966) covalent geometry : angle 0.64775 ( 8100) hydrogen bonds : bond 0.04809 ( 309) hydrogen bonds : angle 5.61045 ( 906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.9258 (t80) cc_final: 0.9018 (t80) REVERT: A 103 GLN cc_start: 0.8439 (tp40) cc_final: 0.7905 (tp40) REVERT: A 137 ASN cc_start: 0.7529 (t0) cc_final: 0.7113 (t0) REVERT: A 156 TRP cc_start: 0.7301 (m-90) cc_final: 0.6916 (m-90) REVERT: A 235 LEU cc_start: 0.7948 (mm) cc_final: 0.7629 (mm) REVERT: A 241 ASP cc_start: 0.8411 (m-30) cc_final: 0.8112 (p0) REVERT: A 248 MET cc_start: 0.9366 (mpp) cc_final: 0.9069 (mpp) REVERT: A 263 MET cc_start: 0.8625 (mtp) cc_final: 0.8270 (mtp) REVERT: A 274 LEU cc_start: 0.9246 (mt) cc_final: 0.8961 (mt) REVERT: A 322 LEU cc_start: 0.8591 (tp) cc_final: 0.8361 (tp) REVERT: A 383 VAL cc_start: 0.9560 (p) cc_final: 0.9356 (p) REVERT: A 387 TYR cc_start: 0.9252 (m-80) cc_final: 0.8987 (m-10) REVERT: A 394 VAL cc_start: 0.8771 (t) cc_final: 0.8483 (t) REVERT: A 412 GLN cc_start: 0.9264 (mt0) cc_final: 0.8841 (mt0) REVERT: A 428 PHE cc_start: 0.8475 (m-80) cc_final: 0.7893 (m-80) REVERT: A 439 ASN cc_start: 0.9237 (t0) cc_final: 0.8708 (t0) REVERT: A 444 TRP cc_start: 0.7782 (m-90) cc_final: 0.6515 (m-90) REVERT: A 467 MET cc_start: 0.6659 (tpp) cc_final: 0.6417 (tpp) REVERT: A 468 PHE cc_start: 0.8652 (m-80) cc_final: 0.7935 (m-80) REVERT: B 19 LEU cc_start: 0.9248 (mt) cc_final: 0.8949 (mt) REVERT: B 62 LEU cc_start: 0.9069 (tp) cc_final: 0.8859 (tp) REVERT: C 4 GLU cc_start: 0.8912 (mp0) cc_final: 0.8128 (tm-30) REVERT: C 9 TYR cc_start: 0.8394 (m-10) cc_final: 0.8066 (m-10) REVERT: C 12 MET cc_start: 0.9226 (tpt) cc_final: 0.8551 (ptt) REVERT: C 24 ASP cc_start: 0.8447 (t0) cc_final: 0.8118 (t0) REVERT: C 27 THR cc_start: 0.7575 (m) cc_final: 0.7347 (m) REVERT: C 35 LEU cc_start: 0.9424 (tp) cc_final: 0.9167 (tp) REVERT: C 52 PHE cc_start: 0.9339 (t80) cc_final: 0.9060 (t80) REVERT: C 55 ASP cc_start: 0.8449 (t70) cc_final: 0.7809 (t0) REVERT: C 75 TRP cc_start: 0.8470 (t60) cc_final: 0.7927 (t60) REVERT: C 82 TYR cc_start: 0.8885 (t80) cc_final: 0.8355 (t80) REVERT: D 15 LEU cc_start: 0.9500 (tp) cc_final: 0.9252 (tp) REVERT: D 17 ASN cc_start: 0.8805 (m-40) cc_final: 0.8348 (m110) REVERT: D 19 LEU cc_start: 0.9579 (mt) cc_final: 0.9239 (mt) REVERT: D 33 ASN cc_start: 0.8756 (m110) cc_final: 0.8400 (m-40) REVERT: D 52 PHE cc_start: 0.9440 (t80) cc_final: 0.9236 (t80) REVERT: D 55 ASP cc_start: 0.8378 (t0) cc_final: 0.7829 (t0) REVERT: D 59 ASP cc_start: 0.9183 (m-30) cc_final: 0.8843 (m-30) REVERT: D 63 LEU cc_start: 0.9476 (mt) cc_final: 0.9153 (mp) REVERT: D 74 GLN cc_start: 0.8905 (mt0) cc_final: 0.7897 (mm110) REVERT: D 89 ILE cc_start: 0.8617 (pt) cc_final: 0.8330 (pt) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.0660 time to fit residues: 21.7202 Evaluate side-chains 185 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 0.0060 chunk 29 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.073350 restraints weight = 24800.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.075690 restraints weight = 15020.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.077293 restraints weight = 10120.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078378 restraints weight = 7411.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.079171 restraints weight = 5835.821| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5966 Z= 0.172 Angle : 0.648 9.934 8100 Z= 0.344 Chirality : 0.043 0.197 835 Planarity : 0.004 0.054 1071 Dihedral : 5.680 73.959 784 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.95 % Favored : 97.91 % Rotamer: Outliers : 0.16 % Allowed : 2.13 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.26 (0.32), residues: 717 helix: 1.37 (0.26), residues: 407 sheet: 0.75 (0.74), residues: 44 loop : 0.16 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 98 TYR 0.021 0.002 TYR B 9 PHE 0.024 0.002 PHE C 25 TRP 0.032 0.003 TRP B 75 HIS 0.005 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5966) covalent geometry : angle 0.64848 ( 8100) hydrogen bonds : bond 0.04155 ( 309) hydrogen bonds : angle 5.27489 ( 906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8270 (m-80) cc_final: 0.7864 (m-80) REVERT: A 64 PHE cc_start: 0.9235 (t80) cc_final: 0.8962 (t80) REVERT: A 103 GLN cc_start: 0.8531 (tp40) cc_final: 0.7910 (tp40) REVERT: A 137 ASN cc_start: 0.7562 (t0) cc_final: 0.6980 (t0) REVERT: A 138 MET cc_start: 0.7410 (mmp) cc_final: 0.6936 (mmm) REVERT: A 229 ASP cc_start: 0.8787 (m-30) cc_final: 0.8541 (m-30) REVERT: A 241 ASP cc_start: 0.8656 (m-30) cc_final: 0.8296 (p0) REVERT: A 248 MET cc_start: 0.9297 (mpp) cc_final: 0.9079 (mpp) REVERT: A 270 GLU cc_start: 0.9025 (tp30) cc_final: 0.8687 (tp30) REVERT: A 274 LEU cc_start: 0.9566 (mt) cc_final: 0.9349 (mt) REVERT: A 322 LEU cc_start: 0.8901 (tp) cc_final: 0.8671 (tp) REVERT: A 330 ILE cc_start: 0.8265 (mt) cc_final: 0.8035 (mt) REVERT: A 384 TRP cc_start: 0.9415 (p-90) cc_final: 0.8905 (p-90) REVERT: A 412 GLN cc_start: 0.9515 (mt0) cc_final: 0.9160 (mt0) REVERT: A 428 PHE cc_start: 0.8182 (m-80) cc_final: 0.7885 (m-80) REVERT: A 433 PHE cc_start: 0.9227 (p90) cc_final: 0.8990 (p90) REVERT: A 434 LEU cc_start: 0.9304 (mt) cc_final: 0.9056 (mt) REVERT: A 437 ASN cc_start: 0.8566 (p0) cc_final: 0.7436 (p0) REVERT: A 439 ASN cc_start: 0.9376 (t0) cc_final: 0.8909 (t0) REVERT: B 12 MET cc_start: 0.8793 (tmm) cc_final: 0.8066 (mtt) REVERT: B 19 LEU cc_start: 0.9126 (mt) cc_final: 0.8756 (mt) REVERT: B 24 ASP cc_start: 0.7694 (t0) cc_final: 0.5742 (t0) REVERT: C 4 GLU cc_start: 0.9196 (mp0) cc_final: 0.8330 (tm-30) REVERT: C 9 TYR cc_start: 0.8416 (m-10) cc_final: 0.8074 (m-10) REVERT: C 12 MET cc_start: 0.9277 (tpt) cc_final: 0.8902 (ptt) REVERT: C 16 PHE cc_start: 0.9532 (t80) cc_final: 0.9129 (t80) REVERT: C 19 LEU cc_start: 0.9571 (mt) cc_final: 0.9212 (mt) REVERT: C 20 GLN cc_start: 0.9087 (tt0) cc_final: 0.8452 (mt0) REVERT: C 24 ASP cc_start: 0.9022 (t0) cc_final: 0.8364 (t0) REVERT: C 27 THR cc_start: 0.7620 (m) cc_final: 0.6553 (m) REVERT: C 34 LEU cc_start: 0.9181 (tp) cc_final: 0.8924 (tp) REVERT: C 41 LEU cc_start: 0.9688 (mt) cc_final: 0.9472 (mt) REVERT: C 55 ASP cc_start: 0.8343 (t70) cc_final: 0.7849 (t0) REVERT: C 57 ASN cc_start: 0.8816 (t0) cc_final: 0.8573 (t0) REVERT: C 66 LEU cc_start: 0.9350 (pp) cc_final: 0.9129 (pp) REVERT: C 77 PHE cc_start: 0.8668 (t80) cc_final: 0.8329 (t80) REVERT: C 79 LYS cc_start: 0.9430 (tttt) cc_final: 0.9175 (pttt) REVERT: C 82 TYR cc_start: 0.9125 (t80) cc_final: 0.8748 (t80) REVERT: D 15 LEU cc_start: 0.9635 (tp) cc_final: 0.9359 (tp) REVERT: D 17 ASN cc_start: 0.8990 (m-40) cc_final: 0.8599 (m110) REVERT: D 33 ASN cc_start: 0.8795 (m110) cc_final: 0.8481 (m110) REVERT: D 52 PHE cc_start: 0.9456 (t80) cc_final: 0.9189 (t80) REVERT: D 55 ASP cc_start: 0.8347 (t0) cc_final: 0.7858 (t0) REVERT: D 59 ASP cc_start: 0.9332 (m-30) cc_final: 0.9110 (m-30) REVERT: D 63 LEU cc_start: 0.9670 (mt) cc_final: 0.9349 (mt) REVERT: D 66 LEU cc_start: 0.9483 (mt) cc_final: 0.9183 (mt) REVERT: D 70 ASP cc_start: 0.7986 (t70) cc_final: 0.7158 (t0) REVERT: D 74 GLN cc_start: 0.8961 (mt0) cc_final: 0.8075 (mm-40) REVERT: D 79 LYS cc_start: 0.9101 (ptpt) cc_final: 0.8769 (ptpp) outliers start: 1 outliers final: 1 residues processed: 231 average time/residue: 0.0633 time to fit residues: 19.7901 Evaluate side-chains 176 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS A 461 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 20 GLN C 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072716 restraints weight = 24590.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075045 restraints weight = 14746.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076641 restraints weight = 9939.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077780 restraints weight = 7295.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078538 restraints weight = 5736.305| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5966 Z= 0.152 Angle : 0.615 9.528 8100 Z= 0.322 Chirality : 0.042 0.185 835 Planarity : 0.004 0.048 1071 Dihedral : 6.300 87.846 784 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.37 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.22 (0.32), residues: 717 helix: 1.41 (0.26), residues: 406 sheet: 0.10 (0.72), residues: 50 loop : 0.14 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 98 TYR 0.014 0.001 TYR C 45 PHE 0.016 0.002 PHE D 25 TRP 0.040 0.002 TRP A 156 HIS 0.006 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5966) covalent geometry : angle 0.61455 ( 8100) hydrogen bonds : bond 0.03817 ( 309) hydrogen bonds : angle 5.08517 ( 906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8457 (m-80) cc_final: 0.8048 (m-80) REVERT: A 64 PHE cc_start: 0.9219 (t80) cc_final: 0.9000 (t80) REVERT: A 103 GLN cc_start: 0.8541 (tp40) cc_final: 0.7886 (tm-30) REVERT: A 137 ASN cc_start: 0.7341 (t0) cc_final: 0.6761 (t0) REVERT: A 138 MET cc_start: 0.7441 (mmp) cc_final: 0.6932 (mmm) REVERT: A 241 ASP cc_start: 0.8428 (m-30) cc_final: 0.7980 (p0) REVERT: A 248 MET cc_start: 0.9224 (mpp) cc_final: 0.8955 (mpp) REVERT: A 270 GLU cc_start: 0.8957 (tp30) cc_final: 0.8729 (tp30) REVERT: A 311 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7804 (mtm110) REVERT: A 350 ASP cc_start: 0.8520 (m-30) cc_final: 0.8215 (m-30) REVERT: A 357 LEU cc_start: 0.9334 (tp) cc_final: 0.9075 (tp) REVERT: A 412 GLN cc_start: 0.9484 (mt0) cc_final: 0.9098 (mt0) REVERT: A 428 PHE cc_start: 0.8332 (m-80) cc_final: 0.8065 (m-80) REVERT: A 434 LEU cc_start: 0.9285 (mt) cc_final: 0.9084 (mt) REVERT: A 437 ASN cc_start: 0.8551 (p0) cc_final: 0.7209 (p0) REVERT: A 439 ASN cc_start: 0.9466 (t0) cc_final: 0.8860 (t0) REVERT: A 451 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 467 MET cc_start: 0.8717 (ttm) cc_final: 0.8228 (ttm) REVERT: B 12 MET cc_start: 0.8821 (tmm) cc_final: 0.8155 (mtt) REVERT: B 13 LEU cc_start: 0.9345 (tp) cc_final: 0.8824 (tp) REVERT: B 19 LEU cc_start: 0.9217 (mt) cc_final: 0.8977 (mt) REVERT: B 20 GLN cc_start: 0.8287 (tp40) cc_final: 0.7007 (tp-100) REVERT: B 24 ASP cc_start: 0.7551 (t0) cc_final: 0.5632 (t0) REVERT: B 75 TRP cc_start: 0.9103 (t-100) cc_final: 0.8872 (t-100) REVERT: B 89 ILE cc_start: 0.7377 (pt) cc_final: 0.7168 (pt) REVERT: C 4 GLU cc_start: 0.9153 (mp0) cc_final: 0.8371 (tm-30) REVERT: C 9 TYR cc_start: 0.8577 (m-10) cc_final: 0.8061 (m-10) REVERT: C 12 MET cc_start: 0.9347 (tpt) cc_final: 0.9006 (ptt) REVERT: C 16 PHE cc_start: 0.9478 (t80) cc_final: 0.9190 (t80) REVERT: C 20 GLN cc_start: 0.9157 (mt0) cc_final: 0.8918 (mt0) REVERT: C 24 ASP cc_start: 0.8913 (t0) cc_final: 0.8499 (t0) REVERT: C 27 THR cc_start: 0.8128 (m) cc_final: 0.6303 (m) REVERT: C 30 ASN cc_start: 0.9247 (m-40) cc_final: 0.8889 (m-40) REVERT: C 34 LEU cc_start: 0.9215 (tp) cc_final: 0.8980 (tp) REVERT: C 46 ASN cc_start: 0.8824 (p0) cc_final: 0.8564 (p0) REVERT: C 55 ASP cc_start: 0.8507 (t70) cc_final: 0.8104 (t0) REVERT: C 77 PHE cc_start: 0.8588 (t80) cc_final: 0.8342 (t80) REVERT: C 78 TYR cc_start: 0.8714 (t80) cc_final: 0.8395 (t80) REVERT: D 12 MET cc_start: 0.9209 (tpt) cc_final: 0.8874 (tpt) REVERT: D 15 LEU cc_start: 0.9690 (tp) cc_final: 0.9405 (tp) REVERT: D 17 ASN cc_start: 0.9066 (m-40) cc_final: 0.8654 (m110) REVERT: D 19 LEU cc_start: 0.9500 (mt) cc_final: 0.9249 (mt) REVERT: D 33 ASN cc_start: 0.8817 (m110) cc_final: 0.8490 (m110) REVERT: D 52 PHE cc_start: 0.9432 (t80) cc_final: 0.9091 (t80) REVERT: D 55 ASP cc_start: 0.8288 (t0) cc_final: 0.6969 (t0) REVERT: D 60 LYS cc_start: 0.9138 (pttt) cc_final: 0.8111 (pttt) REVERT: D 63 LEU cc_start: 0.9716 (mt) cc_final: 0.9481 (mt) REVERT: D 66 LEU cc_start: 0.9366 (mt) cc_final: 0.9153 (mt) REVERT: D 74 GLN cc_start: 0.8960 (mt0) cc_final: 0.7922 (mm-40) REVERT: D 89 ILE cc_start: 0.9333 (pt) cc_final: 0.9114 (pt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0675 time to fit residues: 20.6036 Evaluate side-chains 178 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 30.0000 chunk 69 optimal weight: 0.0970 chunk 17 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN D 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072961 restraints weight = 25452.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.075321 restraints weight = 15232.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076894 restraints weight = 10220.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078009 restraints weight = 7485.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078748 restraints weight = 5875.420| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5966 Z= 0.128 Angle : 0.605 8.661 8100 Z= 0.318 Chirality : 0.041 0.182 835 Planarity : 0.004 0.035 1071 Dihedral : 6.254 89.134 784 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.51 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.08 (0.32), residues: 717 helix: 1.33 (0.26), residues: 406 sheet: 0.13 (0.72), residues: 50 loop : -0.00 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 277 TYR 0.014 0.002 TYR A 438 PHE 0.014 0.002 PHE C 52 TRP 0.044 0.002 TRP A 156 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5966) covalent geometry : angle 0.60502 ( 8100) hydrogen bonds : bond 0.03637 ( 309) hydrogen bonds : angle 4.93914 ( 906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8125 (t0) cc_final: 0.7917 (t0) REVERT: A 19 PHE cc_start: 0.8341 (m-80) cc_final: 0.7997 (m-10) REVERT: A 103 GLN cc_start: 0.8601 (tp40) cc_final: 0.8043 (tp40) REVERT: A 137 ASN cc_start: 0.7316 (t0) cc_final: 0.6740 (t0) REVERT: A 138 MET cc_start: 0.7371 (mmp) cc_final: 0.6827 (mmm) REVERT: A 241 ASP cc_start: 0.8523 (m-30) cc_final: 0.7988 (p0) REVERT: A 248 MET cc_start: 0.9248 (mpp) cc_final: 0.8927 (mpp) REVERT: A 270 GLU cc_start: 0.9028 (tp30) cc_final: 0.8677 (tp30) REVERT: A 274 LEU cc_start: 0.9473 (mt) cc_final: 0.9262 (mt) REVERT: A 322 LEU cc_start: 0.8928 (tp) cc_final: 0.8677 (tp) REVERT: A 357 LEU cc_start: 0.9314 (tp) cc_final: 0.9019 (tp) REVERT: A 412 GLN cc_start: 0.9430 (mt0) cc_final: 0.9185 (mt0) REVERT: A 433 PHE cc_start: 0.9036 (p90) cc_final: 0.8828 (p90) REVERT: A 437 ASN cc_start: 0.8480 (p0) cc_final: 0.7428 (p0) REVERT: A 439 ASN cc_start: 0.9394 (t0) cc_final: 0.8890 (t0) REVERT: A 465 ASN cc_start: 0.7685 (t0) cc_final: 0.7063 (t0) REVERT: A 467 MET cc_start: 0.8611 (ttm) cc_final: 0.8253 (ttm) REVERT: B 12 MET cc_start: 0.8726 (tmm) cc_final: 0.8096 (mtt) REVERT: B 19 LEU cc_start: 0.9312 (mt) cc_final: 0.8971 (mt) REVERT: B 24 ASP cc_start: 0.7868 (t0) cc_final: 0.6982 (t0) REVERT: B 75 TRP cc_start: 0.9230 (t-100) cc_final: 0.8784 (t-100) REVERT: B 89 ILE cc_start: 0.7246 (pt) cc_final: 0.7014 (pt) REVERT: C 4 GLU cc_start: 0.9153 (mp0) cc_final: 0.8035 (tm-30) REVERT: C 9 TYR cc_start: 0.8542 (m-10) cc_final: 0.8099 (m-10) REVERT: C 12 MET cc_start: 0.9327 (tpt) cc_final: 0.9010 (ptt) REVERT: C 20 GLN cc_start: 0.9199 (mt0) cc_final: 0.8995 (mt0) REVERT: C 27 THR cc_start: 0.8111 (m) cc_final: 0.6606 (m) REVERT: C 30 ASN cc_start: 0.9305 (m-40) cc_final: 0.9006 (m-40) REVERT: C 46 ASN cc_start: 0.8815 (p0) cc_final: 0.8568 (p0) REVERT: C 55 ASP cc_start: 0.8543 (t70) cc_final: 0.8129 (t0) REVERT: C 78 TYR cc_start: 0.8744 (t80) cc_final: 0.7949 (t80) REVERT: D 12 MET cc_start: 0.9254 (tpt) cc_final: 0.8957 (tpt) REVERT: D 17 ASN cc_start: 0.9257 (m-40) cc_final: 0.8931 (m110) REVERT: D 19 LEU cc_start: 0.9561 (mt) cc_final: 0.9279 (mt) REVERT: D 33 ASN cc_start: 0.8940 (m110) cc_final: 0.8632 (m110) REVERT: D 42 LEU cc_start: 0.8941 (mt) cc_final: 0.8666 (mt) REVERT: D 52 PHE cc_start: 0.9420 (t80) cc_final: 0.9163 (t80) REVERT: D 55 ASP cc_start: 0.8366 (t0) cc_final: 0.7201 (t0) REVERT: D 60 LYS cc_start: 0.9158 (pttt) cc_final: 0.8327 (pttt) REVERT: D 66 LEU cc_start: 0.9515 (mt) cc_final: 0.9174 (mt) REVERT: D 74 GLN cc_start: 0.9009 (mt0) cc_final: 0.8085 (mm110) REVERT: D 81 PHE cc_start: 0.8265 (t80) cc_final: 0.7914 (t80) REVERT: D 84 ASN cc_start: 0.8501 (t0) cc_final: 0.8239 (t0) REVERT: D 89 ILE cc_start: 0.9375 (pt) cc_final: 0.9086 (mp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.0701 time to fit residues: 20.2324 Evaluate side-chains 186 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071514 restraints weight = 24998.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073815 restraints weight = 14997.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.075379 restraints weight = 10078.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076471 restraints weight = 7364.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077251 restraints weight = 5772.806| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5966 Z= 0.148 Angle : 0.613 7.549 8100 Z= 0.322 Chirality : 0.041 0.192 835 Planarity : 0.004 0.036 1071 Dihedral : 6.291 86.477 784 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.35 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.93 (0.31), residues: 717 helix: 1.21 (0.26), residues: 407 sheet: 0.03 (0.71), residues: 52 loop : -0.06 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 277 TYR 0.014 0.002 TYR A 410 PHE 0.028 0.002 PHE C 52 TRP 0.025 0.002 TRP A 156 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5966) covalent geometry : angle 0.61311 ( 8100) hydrogen bonds : bond 0.03833 ( 309) hydrogen bonds : angle 4.91301 ( 906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8285 (t0) cc_final: 0.8017 (t0) REVERT: A 19 PHE cc_start: 0.8434 (m-80) cc_final: 0.8104 (m-80) REVERT: A 64 PHE cc_start: 0.9132 (t80) cc_final: 0.8931 (t80) REVERT: A 137 ASN cc_start: 0.7322 (t0) cc_final: 0.6584 (t0) REVERT: A 138 MET cc_start: 0.7421 (mmp) cc_final: 0.6881 (mmm) REVERT: A 241 ASP cc_start: 0.8594 (m-30) cc_final: 0.8216 (p0) REVERT: A 248 MET cc_start: 0.9213 (mpp) cc_final: 0.8986 (mpp) REVERT: A 270 GLU cc_start: 0.9102 (tp30) cc_final: 0.8713 (tp30) REVERT: A 322 LEU cc_start: 0.8879 (tp) cc_final: 0.8610 (tp) REVERT: A 357 LEU cc_start: 0.9358 (tp) cc_final: 0.8946 (tp) REVERT: A 412 GLN cc_start: 0.9419 (mt0) cc_final: 0.9139 (mt0) REVERT: A 428 PHE cc_start: 0.8099 (m-80) cc_final: 0.7833 (m-80) REVERT: A 437 ASN cc_start: 0.8558 (p0) cc_final: 0.7419 (p0) REVERT: A 439 ASN cc_start: 0.9452 (t0) cc_final: 0.8800 (t0) REVERT: A 467 MET cc_start: 0.8716 (ttm) cc_final: 0.8222 (ttm) REVERT: B 12 MET cc_start: 0.8727 (tmm) cc_final: 0.8153 (mtt) REVERT: B 24 ASP cc_start: 0.7443 (t0) cc_final: 0.6875 (t0) REVERT: C 10 THR cc_start: 0.9329 (m) cc_final: 0.9111 (p) REVERT: C 11 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8627 (mt-10) REVERT: C 27 THR cc_start: 0.8296 (m) cc_final: 0.6976 (m) REVERT: C 30 ASN cc_start: 0.9291 (m-40) cc_final: 0.8993 (m-40) REVERT: C 33 ASN cc_start: 0.9064 (m-40) cc_final: 0.8862 (m-40) REVERT: C 57 ASN cc_start: 0.8970 (t0) cc_final: 0.8733 (t0) REVERT: C 78 TYR cc_start: 0.8537 (t80) cc_final: 0.8315 (t80) REVERT: D 15 LEU cc_start: 0.9661 (tp) cc_final: 0.9422 (tp) REVERT: D 16 PHE cc_start: 0.9573 (t80) cc_final: 0.9319 (t80) REVERT: D 17 ASN cc_start: 0.9278 (m-40) cc_final: 0.8968 (m110) REVERT: D 19 LEU cc_start: 0.9525 (mt) cc_final: 0.9125 (mt) REVERT: D 33 ASN cc_start: 0.9034 (m110) cc_final: 0.8719 (m110) REVERT: D 55 ASP cc_start: 0.8304 (t0) cc_final: 0.7102 (t0) REVERT: D 60 LYS cc_start: 0.9220 (pttt) cc_final: 0.8327 (pttt) REVERT: D 74 GLN cc_start: 0.9113 (mt0) cc_final: 0.8182 (mm110) REVERT: D 81 PHE cc_start: 0.8223 (t80) cc_final: 0.7941 (t80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0681 time to fit residues: 19.1385 Evaluate side-chains 170 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 39 GLN D 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071858 restraints weight = 25506.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074124 restraints weight = 14922.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075689 restraints weight = 10015.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076770 restraints weight = 7316.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077467 restraints weight = 5722.083| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.8270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5966 Z= 0.141 Angle : 0.633 7.770 8100 Z= 0.330 Chirality : 0.043 0.211 835 Planarity : 0.004 0.036 1071 Dihedral : 6.260 89.279 784 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.21 % Favored : 96.51 % Rotamer: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.76 (0.31), residues: 717 helix: 1.09 (0.26), residues: 406 sheet: 0.11 (0.72), residues: 52 loop : -0.21 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 277 TYR 0.015 0.001 TYR C 78 PHE 0.021 0.002 PHE C 52 TRP 0.053 0.002 TRP A 156 HIS 0.006 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5966) covalent geometry : angle 0.63258 ( 8100) hydrogen bonds : bond 0.03737 ( 309) hydrogen bonds : angle 5.01087 ( 906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8444 (m-80) cc_final: 0.8184 (m-80) REVERT: A 64 PHE cc_start: 0.9182 (t80) cc_final: 0.8977 (t80) REVERT: A 137 ASN cc_start: 0.7263 (t0) cc_final: 0.6566 (t0) REVERT: A 138 MET cc_start: 0.7543 (mmp) cc_final: 0.7042 (mmm) REVERT: A 221 GLU cc_start: 0.9235 (tp30) cc_final: 0.8907 (tp30) REVERT: A 241 ASP cc_start: 0.8676 (m-30) cc_final: 0.8272 (p0) REVERT: A 242 LYS cc_start: 0.9181 (mmpt) cc_final: 0.8926 (mmmt) REVERT: A 248 MET cc_start: 0.9188 (mpp) cc_final: 0.8890 (mpp) REVERT: A 257 ASN cc_start: 0.8609 (t0) cc_final: 0.8345 (t0) REVERT: A 270 GLU cc_start: 0.9011 (tp30) cc_final: 0.8672 (tp30) REVERT: A 274 LEU cc_start: 0.9526 (mt) cc_final: 0.9055 (mt) REVERT: A 322 LEU cc_start: 0.8893 (tp) cc_final: 0.8613 (tp) REVERT: A 357 LEU cc_start: 0.9374 (tp) cc_final: 0.8969 (tp) REVERT: A 412 GLN cc_start: 0.9387 (mt0) cc_final: 0.9137 (mt0) REVERT: A 428 PHE cc_start: 0.8282 (m-80) cc_final: 0.7904 (m-80) REVERT: A 437 ASN cc_start: 0.8644 (p0) cc_final: 0.7767 (p0) REVERT: A 439 ASN cc_start: 0.9467 (t0) cc_final: 0.8780 (t0) REVERT: A 467 MET cc_start: 0.8646 (ttm) cc_final: 0.8163 (ttm) REVERT: B 12 MET cc_start: 0.8744 (tmm) cc_final: 0.8144 (mtt) REVERT: B 13 LEU cc_start: 0.9401 (tp) cc_final: 0.8982 (tp) REVERT: B 75 TRP cc_start: 0.9135 (t-100) cc_final: 0.8644 (t-100) REVERT: B 89 ILE cc_start: 0.7504 (pt) cc_final: 0.6959 (pt) REVERT: C 13 LEU cc_start: 0.9538 (tp) cc_final: 0.9263 (tp) REVERT: C 30 ASN cc_start: 0.9433 (m-40) cc_final: 0.9215 (m-40) REVERT: C 57 ASN cc_start: 0.9023 (t0) cc_final: 0.8767 (t0) REVERT: D 16 PHE cc_start: 0.9491 (t80) cc_final: 0.9241 (t80) REVERT: D 17 ASN cc_start: 0.9283 (m-40) cc_final: 0.8931 (m110) REVERT: D 19 LEU cc_start: 0.9579 (mt) cc_final: 0.9224 (mt) REVERT: D 33 ASN cc_start: 0.9080 (m110) cc_final: 0.8739 (m110) REVERT: D 55 ASP cc_start: 0.8082 (t0) cc_final: 0.7119 (t0) REVERT: D 60 LYS cc_start: 0.9183 (pttt) cc_final: 0.8358 (pttt) REVERT: D 74 GLN cc_start: 0.9108 (mt0) cc_final: 0.8263 (mm-40) REVERT: D 78 TYR cc_start: 0.8430 (t80) cc_final: 0.7872 (t80) REVERT: D 82 TYR cc_start: 0.8713 (t80) cc_final: 0.8501 (t80) REVERT: D 84 ASN cc_start: 0.8798 (t0) cc_final: 0.8589 (t0) REVERT: D 88 HIS cc_start: 0.9078 (m90) cc_final: 0.8496 (m90) REVERT: D 90 PHE cc_start: 0.8106 (m-10) cc_final: 0.7800 (m-10) outliers start: 1 outliers final: 1 residues processed: 214 average time/residue: 0.0697 time to fit residues: 19.7588 Evaluate side-chains 180 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.168 > 50: distance: 27 - 52: 4.931 distance: 35 - 66: 18.493 distance: 47 - 52: 3.615 distance: 52 - 53: 23.070 distance: 53 - 54: 10.784 distance: 53 - 56: 15.385 distance: 54 - 55: 10.422 distance: 54 - 66: 5.139 distance: 56 - 57: 5.954 distance: 57 - 58: 4.019 distance: 57 - 59: 7.551 distance: 58 - 60: 8.406 distance: 59 - 61: 12.181 distance: 61 - 63: 6.301 distance: 62 - 64: 7.409 distance: 63 - 65: 6.068 distance: 64 - 65: 6.491 distance: 66 - 67: 3.531 distance: 67 - 68: 17.613 distance: 68 - 69: 19.172 distance: 68 - 70: 22.883 distance: 70 - 71: 14.260 distance: 71 - 72: 8.651 distance: 71 - 74: 12.798 distance: 72 - 73: 13.188 distance: 72 - 79: 5.636 distance: 74 - 75: 4.438 distance: 75 - 76: 14.903 distance: 76 - 77: 10.213 distance: 77 - 78: 19.597 distance: 79 - 80: 10.794 distance: 80 - 81: 19.554 distance: 80 - 83: 10.634 distance: 81 - 82: 23.668 distance: 81 - 90: 32.530 distance: 83 - 84: 11.979 distance: 84 - 85: 12.236 distance: 85 - 86: 7.517 distance: 86 - 87: 16.017 distance: 90 - 91: 25.267 distance: 91 - 92: 26.435 distance: 91 - 94: 10.326 distance: 92 - 93: 18.508 distance: 92 - 99: 14.521 distance: 94 - 95: 6.341 distance: 95 - 96: 24.864 distance: 96 - 97: 18.805 distance: 96 - 98: 10.447 distance: 99 - 100: 18.313 distance: 99 - 105: 13.679 distance: 100 - 101: 25.013 distance: 100 - 103: 32.707 distance: 101 - 102: 12.286 distance: 101 - 106: 31.021 distance: 103 - 104: 14.291 distance: 104 - 105: 23.658 distance: 106 - 107: 11.766 distance: 107 - 108: 28.917 distance: 107 - 110: 28.948 distance: 108 - 109: 24.822 distance: 108 - 111: 18.136 distance: 111 - 112: 4.552 distance: 112 - 113: 13.473 distance: 112 - 115: 18.591 distance: 113 - 114: 25.945 distance: 113 - 125: 23.912 distance: 115 - 116: 16.465 distance: 116 - 117: 4.138 distance: 116 - 118: 6.534 distance: 118 - 120: 7.805 distance: 118 - 121: 7.683 distance: 119 - 120: 3.263 distance: 120 - 122: 6.175 distance: 121 - 123: 5.584 distance: 122 - 124: 6.859 distance: 123 - 124: 4.394 distance: 125 - 126: 17.848 distance: 126 - 127: 24.131 distance: 126 - 129: 21.918 distance: 127 - 128: 8.456 distance: 127 - 133: 20.489 distance: 129 - 130: 13.260 distance: 130 - 131: 7.404 distance: 130 - 132: 25.354 distance: 133 - 134: 14.803 distance: 134 - 135: 14.783 distance: 134 - 137: 17.359 distance: 135 - 136: 13.279 distance: 135 - 141: 9.321 distance: 137 - 138: 7.812 distance: 138 - 139: 6.172 distance: 138 - 140: 22.162