Starting phenix.real_space_refine on Mon Apr 28 03:19:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hio_34824/04_2025/8hio_34824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hio_34824/04_2025/8hio_34824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hio_34824/04_2025/8hio_34824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hio_34824/04_2025/8hio_34824.map" model { file = "/net/cci-nas-00/data/ceres_data/8hio_34824/04_2025/8hio_34824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hio_34824/04_2025/8hio_34824.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.012 sd= 0.211 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 47 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 3952 2.51 5 N 1281 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6681 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1019 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 12} Link IDs: {'rna2p': 15, 'rna3p': 31} Chain: "A" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4436 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 543} Chain breaks: 2 Chain: "D" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1224 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5151 SG CYS A 552 106.496 33.507 50.395 1.00185.32 S ATOM 5284 SG CYS A 569 106.415 36.312 50.252 1.00190.90 S ATOM 5302 SG CYS A 572 107.743 36.523 47.525 1.00196.84 S Time building chain proxies: 4.74, per 1000 atoms: 0.71 Number of scatterers: 6681 At special positions: 0 Unit cell: (118.101, 99.603, 102.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 47 15.00 Mg 1 11.99 O 1378 8.00 N 1281 7.00 C 3952 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: 2.01 Conformation dependent library (CDL) restraints added in 880.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 569 " Number of angles added : 3 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 61.3% alpha, 12.2% beta 11 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 18 through 52 Processing helix chain 'A' and resid 53 through 85 Processing helix chain 'A' and resid 92 through 119 Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.501A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.575A pdb=" N ARG A 345 " --> pdb=" O PHE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 397 Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.602A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 479 removed outlier: 3.710A pdb=" N TRP A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 518 through 534 removed outlier: 4.114A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.744A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'D' and resid 19 through 52 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 96 through 118 removed outlier: 3.640A pdb=" N ALA D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 145 removed outlier: 3.519A pdb=" N TYR D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 176 removed outlier: 3.598A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 195 removed outlier: 6.716A pdb=" N THR A 299 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 281 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS A 297 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 283 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 295 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 285 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 293 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A 287 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 11 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE A 262 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG A 251 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 264 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 266 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR A 247 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 removed outlier: 5.947A pdb=" N ALA A 328 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 361 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323 removed outlier: 4.142A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568 374 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 2.36 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: 1691 1.33 - 1.45: 1571 1.45 - 1.57: 3522 1.57 - 1.69: 93 1.69 - 1.81: 33 Bond restraints: 6910 Sorted by residual: bond pdb=" C TRP A 261 " pdb=" N ILE A 262 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.34e-02 5.57e+03 4.96e+00 bond pdb=" C ASP A 477 " pdb=" N GLN A 478 " ideal model delta sigma weight residual 1.332 1.311 0.022 1.40e-02 5.10e+03 2.40e+00 bond pdb=" CG LEU A 221 " pdb=" CD1 LEU A 221 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB VAL A 194 " pdb=" CG1 VAL A 194 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB PHE A 443 " pdb=" CG PHE A 443 " ideal model delta sigma weight residual 1.502 1.477 0.025 2.30e-02 1.89e+03 1.22e+00 ... (remaining 6905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 9367 1.82 - 3.64: 205 3.64 - 5.46: 23 5.46 - 7.28: 4 7.28 - 9.10: 2 Bond angle restraints: 9601 Sorted by residual: angle pdb=" N TRP A 440 " pdb=" CA TRP A 440 " pdb=" C TRP A 440 " ideal model delta sigma weight residual 113.12 108.77 4.35 1.25e+00 6.40e-01 1.21e+01 angle pdb=" CA LEU A 369 " pdb=" CB LEU A 369 " pdb=" CG LEU A 369 " ideal model delta sigma weight residual 116.30 107.20 9.10 3.50e+00 8.16e-02 6.75e+00 angle pdb=" C LEU A 318 " pdb=" N GLY A 319 " pdb=" CA GLY A 319 " ideal model delta sigma weight residual 120.51 124.36 -3.85 1.63e+00 3.76e-01 5.57e+00 angle pdb=" C GLN A 453 " pdb=" N GLU A 454 " pdb=" CA GLU A 454 " ideal model delta sigma weight residual 122.42 118.79 3.63 1.55e+00 4.16e-01 5.48e+00 angle pdb=" C ALA A 281 " pdb=" N GLU A 282 " pdb=" CA GLU A 282 " ideal model delta sigma weight residual 122.99 119.73 3.26 1.41e+00 5.03e-01 5.34e+00 ... (remaining 9596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.19: 3719 19.19 - 38.38: 318 38.38 - 57.58: 133 57.58 - 76.77: 68 76.77 - 95.96: 4 Dihedral angle restraints: 4242 sinusoidal: 2150 harmonic: 2092 Sorted by residual: dihedral pdb=" O4' U B 6 " pdb=" C1' U B 6 " pdb=" N1 U B 6 " pdb=" C2 U B 6 " ideal model delta sinusoidal sigma weight residual -160.00 -83.79 -76.21 1 1.50e+01 4.44e-03 3.25e+01 dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -171.33 65.33 1 1.70e+01 3.46e-03 1.94e+01 dihedral pdb=" O4' C B 15 " pdb=" C1' C B 15 " pdb=" N1 C B 15 " pdb=" C2 C B 15 " ideal model delta sinusoidal sigma weight residual -160.00 -104.45 -55.55 1 1.50e+01 4.44e-03 1.85e+01 ... (remaining 4239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 688 0.029 - 0.058: 282 0.058 - 0.087: 86 0.087 - 0.115: 30 0.115 - 0.144: 10 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL A 268 " pdb=" N VAL A 268 " pdb=" C VAL A 268 " pdb=" CB VAL A 268 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL A 361 " pdb=" N VAL A 361 " pdb=" C VAL A 361 " pdb=" CB VAL A 361 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1093 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C GLN A 452 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN A 452 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 453 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 472 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ALA A 472 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 472 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 473 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 459 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LYS A 459 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 459 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA A 460 " 0.011 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 30 2.38 - 3.01: 3883 3.01 - 3.64: 10567 3.64 - 4.27: 15151 4.27 - 4.90: 24433 Nonbonded interactions: 54064 Sorted by model distance: nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 1.744 2.170 nonbonded pdb=" OP2 C B -21 " pdb="MG MG B 101 " model vdw 1.992 2.170 nonbonded pdb=" OP1 G B -7 " pdb=" NZ LYS A 14 " model vdw 2.111 3.120 nonbonded pdb=" OD2 ASP A 466 " pdb=" NE2 GLN A 470 " model vdw 2.147 3.120 nonbonded pdb=" O TRP A 428 " pdb=" OG SER A 436 " model vdw 2.153 3.040 ... (remaining 54059 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 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: 0.070 Set stop_for_unknowns flag: 0.010 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.390 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:4.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6914 Z= 0.255 Angle : 0.884 36.858 9604 Z= 0.391 Chirality : 0.037 0.144 1096 Planarity : 0.004 0.031 1072 Dihedral : 18.515 95.962 2880 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.32), residues: 707 helix: 2.70 (0.25), residues: 421 sheet: -0.24 (0.58), residues: 75 loop : -0.43 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 320 HIS 0.009 0.002 HIS A 7 PHE 0.008 0.001 PHE A 443 TYR 0.019 0.002 TYR A 217 ARG 0.005 0.001 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.17634 ( 402) hydrogen bonds : angle 5.92566 ( 1160) metal coordination : bond 0.03504 ( 4) metal coordination : angle 33.04508 ( 3) covalent geometry : bond 0.00531 ( 6910) covalent geometry : angle 0.66388 ( 9601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.612 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: A 33 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 138 LYS cc_start: 0.8899 (tttt) cc_final: 0.8609 (tmtt) REVERT: A 169 ILE cc_start: 0.8917 (mm) cc_final: 0.8404 (tp) REVERT: A 333 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7792 (tpp80) REVERT: A 356 SER cc_start: 0.7773 (t) cc_final: 0.7543 (p) REVERT: A 420 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.5416 (mpp-170) REVERT: A 530 MET cc_start: 0.8057 (mmt) cc_final: 0.7515 (mmm) REVERT: D 27 LEU cc_start: 0.9226 (mt) cc_final: 0.8976 (mt) REVERT: D 32 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8005 (ttp-170) REVERT: D 42 TYR cc_start: 0.8057 (t80) cc_final: 0.7857 (t80) REVERT: D 46 LEU cc_start: 0.9019 (mt) cc_final: 0.8653 (mt) REVERT: D 50 TRP cc_start: 0.8448 (m100) cc_final: 0.8030 (m100) REVERT: D 98 ARG cc_start: 0.4191 (mtt180) cc_final: 0.3519 (tpm170) REVERT: D 115 ILE cc_start: 0.4875 (mt) cc_final: 0.4406 (mt) REVERT: D 127 LYS cc_start: 0.9577 (tppt) cc_final: 0.9344 (tptp) REVERT: D 163 LYS cc_start: 0.8615 (mttt) cc_final: 0.8395 (mmtt) REVERT: D 185 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7354 (mtp180) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3130 time to fit residues: 70.5030 Evaluate side-chains 121 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 449 GLN A 516 HIS D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.174451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.135821 restraints weight = 14536.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.140293 restraints weight = 7516.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.143305 restraints weight = 5017.526| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6914 Z= 0.220 Angle : 0.688 13.210 9604 Z= 0.355 Chirality : 0.040 0.173 1096 Planarity : 0.005 0.054 1072 Dihedral : 18.740 98.253 1546 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.44 % Allowed : 19.10 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.33), residues: 707 helix: 2.67 (0.24), residues: 426 sheet: -0.06 (0.62), residues: 73 loop : -0.37 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 450 HIS 0.012 0.002 HIS D 161 PHE 0.008 0.001 PHE A 155 TYR 0.020 0.002 TYR A 217 ARG 0.013 0.001 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.05376 ( 402) hydrogen bonds : angle 4.58706 ( 1160) metal coordination : bond 0.02624 ( 4) metal coordination : angle 7.78070 ( 3) covalent geometry : bond 0.00479 ( 6910) covalent geometry : angle 0.67464 ( 9601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.682 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: A 9 MET cc_start: 0.8153 (mtt) cc_final: 0.7863 (mtm) REVERT: A 29 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7254 (t-90) REVERT: A 53 TYR cc_start: 0.7295 (m-10) cc_final: 0.6901 (m-10) REVERT: A 138 LYS cc_start: 0.8748 (tttt) cc_final: 0.8536 (tmtt) REVERT: A 169 ILE cc_start: 0.8636 (mm) cc_final: 0.7977 (tp) REVERT: A 356 SER cc_start: 0.7632 (t) cc_final: 0.7348 (p) REVERT: A 420 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.5433 (mpp-170) REVERT: D 23 GLN cc_start: 0.8847 (tp40) cc_final: 0.8572 (mt0) REVERT: D 32 ARG cc_start: 0.8578 (ttp80) cc_final: 0.7998 (ttp-170) REVERT: D 42 TYR cc_start: 0.8143 (t80) cc_final: 0.7805 (t80) REVERT: D 46 LEU cc_start: 0.9193 (mt) cc_final: 0.8718 (mm) REVERT: D 50 TRP cc_start: 0.8189 (m100) cc_final: 0.7945 (m100) REVERT: D 138 LYS cc_start: 0.9414 (mttt) cc_final: 0.9134 (mttp) REVERT: D 167 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8206 (mmmt) REVERT: D 185 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7396 (mtm180) outliers start: 20 outliers final: 9 residues processed: 138 average time/residue: 0.2866 time to fit residues: 49.7582 Evaluate side-chains 117 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 516 HIS D 29 HIS D 143 GLN D 184 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.170225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.134468 restraints weight = 15031.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.138533 restraints weight = 7957.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.141134 restraints weight = 5417.516| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6914 Z= 0.157 Angle : 0.596 7.513 9604 Z= 0.309 Chirality : 0.038 0.272 1096 Planarity : 0.004 0.038 1072 Dihedral : 18.603 99.257 1546 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.10 % Allowed : 19.97 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.33), residues: 707 helix: 2.80 (0.25), residues: 426 sheet: 0.11 (0.62), residues: 77 loop : -0.25 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 450 HIS 0.011 0.002 HIS D 29 PHE 0.006 0.001 PHE A 582 TYR 0.016 0.002 TYR A 217 ARG 0.004 0.001 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 402) hydrogen bonds : angle 4.25367 ( 1160) metal coordination : bond 0.01457 ( 4) metal coordination : angle 2.49239 ( 3) covalent geometry : bond 0.00339 ( 6910) covalent geometry : angle 0.59400 ( 9601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.106 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: A 9 MET cc_start: 0.8047 (mtt) cc_final: 0.7782 (mtm) REVERT: A 29 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7255 (t-90) REVERT: A 63 MET cc_start: 0.8986 (ptp) cc_final: 0.8358 (ptp) REVERT: A 93 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6550 (tp) REVERT: A 356 SER cc_start: 0.7550 (t) cc_final: 0.7284 (p) REVERT: D 27 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9059 (pp) REVERT: D 42 TYR cc_start: 0.8040 (t80) cc_final: 0.7798 (t80) REVERT: D 46 LEU cc_start: 0.9167 (mt) cc_final: 0.8719 (mm) REVERT: D 127 LYS cc_start: 0.9436 (tppt) cc_final: 0.9057 (tppt) REVERT: D 167 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8200 (mmmt) REVERT: D 185 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7381 (mtm180) outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 0.2890 time to fit residues: 46.8870 Evaluate side-chains 109 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 452 GLN D 29 HIS D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.165563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126487 restraints weight = 14135.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.130665 restraints weight = 7407.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.133407 restraints weight = 4995.543| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 6914 Z= 0.280 Angle : 0.730 9.091 9604 Z= 0.373 Chirality : 0.041 0.205 1096 Planarity : 0.005 0.057 1072 Dihedral : 18.765 99.830 1546 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.68 % Allowed : 21.34 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.33), residues: 707 helix: 2.47 (0.25), residues: 425 sheet: -0.22 (0.66), residues: 71 loop : -0.67 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 450 HIS 0.014 0.002 HIS D 29 PHE 0.008 0.002 PHE A 155 TYR 0.021 0.002 TYR A 217 ARG 0.007 0.001 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.05334 ( 402) hydrogen bonds : angle 4.65531 ( 1160) metal coordination : bond 0.01706 ( 4) metal coordination : angle 2.93695 ( 3) covalent geometry : bond 0.00609 ( 6910) covalent geometry : angle 0.72850 ( 9601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.712 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: A 9 MET cc_start: 0.8197 (mtt) cc_final: 0.7831 (mtm) REVERT: A 29 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7319 (t-90) REVERT: A 93 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6039 (tp) REVERT: D 23 GLN cc_start: 0.8958 (tp40) cc_final: 0.8637 (pt0) REVERT: D 32 ARG cc_start: 0.8544 (ttp80) cc_final: 0.7995 (ttm-80) REVERT: D 115 ILE cc_start: 0.4314 (mt) cc_final: 0.4091 (mt) REVERT: D 127 LYS cc_start: 0.9402 (tppt) cc_final: 0.8982 (tppt) REVERT: D 167 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8358 (mmmt) REVERT: D 185 ARG cc_start: 0.8512 (mmm160) cc_final: 0.7413 (mtm180) outliers start: 33 outliers final: 23 residues processed: 124 average time/residue: 0.2894 time to fit residues: 46.8116 Evaluate side-chains 120 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 137 GLN D 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.170048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.129804 restraints weight = 14010.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.134086 restraints weight = 7367.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137026 restraints weight = 5007.827| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6914 Z= 0.138 Angle : 0.588 11.094 9604 Z= 0.303 Chirality : 0.037 0.168 1096 Planarity : 0.004 0.036 1072 Dihedral : 18.533 101.245 1546 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.48 % Allowed : 23.75 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.33), residues: 707 helix: 2.66 (0.24), residues: 426 sheet: -0.15 (0.65), residues: 71 loop : -0.29 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 450 HIS 0.014 0.001 HIS D 29 PHE 0.005 0.001 PHE A 582 TYR 0.018 0.002 TYR D 42 ARG 0.004 0.000 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 402) hydrogen bonds : angle 4.21338 ( 1160) metal coordination : bond 0.00792 ( 4) metal coordination : angle 2.06143 ( 3) covalent geometry : bond 0.00303 ( 6910) covalent geometry : angle 0.58651 ( 9601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.628 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: A 9 MET cc_start: 0.8123 (mtt) cc_final: 0.7804 (mtm) REVERT: A 29 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7120 (t-90) REVERT: A 185 ARG cc_start: 0.6432 (mtm180) cc_final: 0.5718 (mtm-85) REVERT: A 194 VAL cc_start: 0.7587 (OUTLIER) cc_final: 0.7355 (p) REVERT: A 446 ASP cc_start: 0.7937 (t0) cc_final: 0.7733 (t70) REVERT: A 475 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7572 (mm) REVERT: A 556 ASN cc_start: 0.8615 (m110) cc_final: 0.8063 (m110) REVERT: D 32 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8138 (ttm170) REVERT: D 42 TYR cc_start: 0.8078 (t80) cc_final: 0.7237 (t80) REVERT: D 115 ILE cc_start: 0.4755 (mt) cc_final: 0.4526 (mt) REVERT: D 127 LYS cc_start: 0.9322 (tppt) cc_final: 0.8852 (tppt) REVERT: D 185 ARG cc_start: 0.8515 (mmm160) cc_final: 0.7408 (mtm180) outliers start: 26 outliers final: 16 residues processed: 116 average time/residue: 0.2339 time to fit residues: 34.3697 Evaluate side-chains 109 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 40.0000 chunk 74 optimal weight: 50.0000 chunk 73 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 143 GLN D 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.169854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129880 restraints weight = 13855.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.134198 restraints weight = 7366.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.137019 restraints weight = 4980.688| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6914 Z= 0.167 Angle : 0.618 9.787 9604 Z= 0.318 Chirality : 0.037 0.160 1096 Planarity : 0.004 0.035 1072 Dihedral : 18.508 101.241 1546 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.65 % Allowed : 23.75 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.33), residues: 707 helix: 2.58 (0.24), residues: 426 sheet: -0.19 (0.72), residues: 61 loop : -0.27 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 428 HIS 0.013 0.002 HIS D 29 PHE 0.006 0.001 PHE A 582 TYR 0.015 0.002 TYR A 217 ARG 0.004 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 402) hydrogen bonds : angle 4.19824 ( 1160) metal coordination : bond 0.00898 ( 4) metal coordination : angle 2.23509 ( 3) covalent geometry : bond 0.00369 ( 6910) covalent geometry : angle 0.61677 ( 9601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.636 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: A 9 MET cc_start: 0.8066 (mtt) cc_final: 0.7686 (mtm) REVERT: A 11 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8345 (t) REVERT: A 29 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7183 (t-90) REVERT: A 138 LYS cc_start: 0.8541 (tptt) cc_final: 0.8149 (tptp) REVERT: A 431 ASN cc_start: 0.6967 (p0) cc_final: 0.6657 (p0) REVERT: A 475 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7608 (mm) REVERT: A 575 MET cc_start: 0.8677 (tpp) cc_final: 0.8470 (tpp) REVERT: D 32 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8231 (ttm170) REVERT: D 50 TRP cc_start: 0.8181 (m100) cc_final: 0.7966 (m100) REVERT: D 127 LYS cc_start: 0.9325 (tppt) cc_final: 0.8850 (tppt) REVERT: D 185 ARG cc_start: 0.8495 (mmm160) cc_final: 0.7402 (mtm180) outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 0.2250 time to fit residues: 31.9792 Evaluate side-chains 110 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 50.0000 chunk 56 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 15 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 overall best weight: 4.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS D 30 ASN D 143 GLN D 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.173923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.135363 restraints weight = 14428.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.139641 restraints weight = 7564.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.142501 restraints weight = 5087.367| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6914 Z= 0.190 Angle : 0.638 9.221 9604 Z= 0.328 Chirality : 0.038 0.160 1096 Planarity : 0.004 0.037 1072 Dihedral : 18.505 101.122 1546 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.99 % Allowed : 24.10 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.32), residues: 707 helix: 2.43 (0.24), residues: 426 sheet: -0.45 (0.71), residues: 61 loop : -0.46 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 50 HIS 0.013 0.002 HIS D 29 PHE 0.006 0.001 PHE A 582 TYR 0.017 0.002 TYR A 576 ARG 0.005 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 402) hydrogen bonds : angle 4.25823 ( 1160) metal coordination : bond 0.00397 ( 4) metal coordination : angle 1.77199 ( 3) covalent geometry : bond 0.00419 ( 6910) covalent geometry : angle 0.63686 ( 9601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8159 (mtt) cc_final: 0.7763 (mtm) REVERT: A 11 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8360 (t) REVERT: A 29 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7244 (t-90) REVERT: A 50 TRP cc_start: 0.7567 (m100) cc_final: 0.7292 (m100) REVERT: A 185 ARG cc_start: 0.6516 (mtm180) cc_final: 0.6218 (mtm180) REVERT: A 309 THR cc_start: 0.8538 (p) cc_final: 0.8257 (t) REVERT: A 446 ASP cc_start: 0.8148 (t0) cc_final: 0.7893 (t70) REVERT: A 556 ASN cc_start: 0.8735 (m-40) cc_final: 0.8171 (m110) REVERT: D 23 GLN cc_start: 0.9028 (tp40) cc_final: 0.8659 (pt0) REVERT: D 32 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8221 (ttm-80) REVERT: D 42 TYR cc_start: 0.8121 (t80) cc_final: 0.7779 (t80) REVERT: D 43 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8559 (t70) REVERT: D 44 ASP cc_start: 0.9344 (m-30) cc_final: 0.9048 (p0) REVERT: D 50 TRP cc_start: 0.8270 (m100) cc_final: 0.7944 (m100) REVERT: D 53 TYR cc_start: 0.6069 (m-80) cc_final: 0.5680 (m-80) REVERT: D 127 LYS cc_start: 0.9326 (tppt) cc_final: 0.8832 (tppt) REVERT: D 185 ARG cc_start: 0.8523 (mmm160) cc_final: 0.7394 (mtm180) outliers start: 29 outliers final: 21 residues processed: 112 average time/residue: 0.2178 time to fit residues: 31.6749 Evaluate side-chains 120 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS D 30 ASN D 95 GLN D 143 GLN D 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.172275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.133953 restraints weight = 13783.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.138240 restraints weight = 7166.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.141077 restraints weight = 4789.369| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6914 Z= 0.120 Angle : 0.610 17.577 9604 Z= 0.307 Chirality : 0.036 0.166 1096 Planarity : 0.004 0.036 1072 Dihedral : 18.351 101.582 1546 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.79 % Allowed : 24.96 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.32), residues: 707 helix: 2.53 (0.24), residues: 432 sheet: -0.40 (0.64), residues: 72 loop : -0.58 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 50 HIS 0.013 0.001 HIS D 29 PHE 0.012 0.001 PHE A 582 TYR 0.018 0.002 TYR D 141 ARG 0.004 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 402) hydrogen bonds : angle 3.97499 ( 1160) metal coordination : bond 0.00465 ( 4) metal coordination : angle 1.05490 ( 3) covalent geometry : bond 0.00266 ( 6910) covalent geometry : angle 0.61009 ( 9601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.810 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: A 9 MET cc_start: 0.7756 (mtt) cc_final: 0.7426 (mtm) REVERT: A 11 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8160 (t) REVERT: A 29 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.7107 (t-90) REVERT: A 138 LYS cc_start: 0.8560 (tptt) cc_final: 0.8187 (tptp) REVERT: A 194 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7533 (p) REVERT: A 309 THR cc_start: 0.8418 (p) cc_final: 0.8143 (t) REVERT: A 556 ASN cc_start: 0.8642 (m-40) cc_final: 0.8187 (m110) REVERT: D 32 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8257 (ttm-80) REVERT: D 42 TYR cc_start: 0.7995 (t80) cc_final: 0.7735 (t80) REVERT: D 127 LYS cc_start: 0.9316 (tppt) cc_final: 0.8825 (tppt) REVERT: D 184 HIS cc_start: 0.6439 (m-70) cc_final: 0.6221 (m-70) REVERT: D 185 ARG cc_start: 0.8484 (mmm160) cc_final: 0.7395 (mtm180) outliers start: 22 outliers final: 13 residues processed: 109 average time/residue: 0.2514 time to fit residues: 35.8379 Evaluate side-chains 107 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 74 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS D 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.169801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.130365 restraints weight = 14012.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.134585 restraints weight = 7352.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.137358 restraints weight = 4948.837| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6914 Z= 0.158 Angle : 0.660 17.250 9604 Z= 0.329 Chirality : 0.038 0.196 1096 Planarity : 0.004 0.037 1072 Dihedral : 18.414 101.845 1546 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.44 % Allowed : 25.65 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.33), residues: 707 helix: 2.41 (0.25), residues: 432 sheet: -0.48 (0.66), residues: 71 loop : -0.61 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 50 HIS 0.013 0.001 HIS D 29 PHE 0.009 0.001 PHE A 582 TYR 0.017 0.002 TYR D 141 ARG 0.005 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 402) hydrogen bonds : angle 4.17727 ( 1160) metal coordination : bond 0.00304 ( 4) metal coordination : angle 1.07362 ( 3) covalent geometry : bond 0.00357 ( 6910) covalent geometry : angle 0.66016 ( 9601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.638 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: A 9 MET cc_start: 0.7997 (mtt) cc_final: 0.7620 (mtm) REVERT: A 29 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7278 (t-90) REVERT: A 138 LYS cc_start: 0.8555 (tptt) cc_final: 0.8185 (tptp) REVERT: A 194 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7344 (p) REVERT: A 309 THR cc_start: 0.8449 (p) cc_final: 0.8170 (t) REVERT: D 23 GLN cc_start: 0.9041 (tp40) cc_final: 0.8729 (mp10) REVERT: D 32 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8292 (ttm-80) REVERT: D 42 TYR cc_start: 0.7990 (t80) cc_final: 0.7717 (t80) REVERT: D 44 ASP cc_start: 0.9272 (m-30) cc_final: 0.8981 (p0) REVERT: D 50 TRP cc_start: 0.8071 (m100) cc_final: 0.6952 (m100) REVERT: D 184 HIS cc_start: 0.6493 (m-70) cc_final: 0.6264 (m-70) REVERT: D 185 ARG cc_start: 0.8513 (mmm160) cc_final: 0.7386 (mtm180) outliers start: 20 outliers final: 14 residues processed: 102 average time/residue: 0.2320 time to fit residues: 30.2826 Evaluate side-chains 104 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.8867 > 50: distance: 2 - 31: 25.937 distance: 12 - 36: 36.707 distance: 18 - 47: 30.249 distance: 25 - 31: 29.284 distance: 26 - 55: 34.733 distance: 31 - 32: 12.114 distance: 32 - 33: 46.350 distance: 32 - 35: 18.279 distance: 33 - 34: 38.891 distance: 33 - 36: 40.822 distance: 34 - 64: 44.442 distance: 36 - 37: 38.559 distance: 37 - 38: 39.186 distance: 37 - 40: 40.506 distance: 38 - 39: 56.062 distance: 38 - 47: 10.443 distance: 39 - 69: 58.534 distance: 40 - 41: 50.207 distance: 41 - 42: 15.793 distance: 42 - 43: 35.929 distance: 44 - 45: 16.084 distance: 44 - 46: 46.143 distance: 47 - 48: 31.871 distance: 48 - 49: 43.128 distance: 48 - 51: 48.708 distance: 49 - 50: 47.979 distance: 49 - 55: 42.121 distance: 51 - 52: 57.608 distance: 51 - 53: 45.650 distance: 52 - 54: 41.951 distance: 55 - 56: 41.243 distance: 56 - 57: 52.006 distance: 56 - 59: 18.490 distance: 57 - 64: 41.181 distance: 59 - 60: 43.269 distance: 60 - 61: 55.504 distance: 61 - 62: 40.359 distance: 64 - 65: 48.358 distance: 65 - 66: 17.352 distance: 65 - 68: 36.803 distance: 66 - 67: 39.157 distance: 66 - 69: 38.895 distance: 69 - 70: 46.361 distance: 70 - 71: 20.489 distance: 70 - 73: 40.836 distance: 71 - 72: 43.715 distance: 71 - 80: 14.272 distance: 73 - 74: 15.431 distance: 74 - 75: 6.077 distance: 76 - 77: 13.347 distance: 77 - 79: 24.797 distance: 80 - 81: 10.302 distance: 81 - 84: 13.739 distance: 82 - 83: 30.449 distance: 84 - 85: 40.474 distance: 86 - 87: 40.031 distance: 87 - 90: 57.041 distance: 88 - 89: 55.742 distance: 88 - 93: 39.477 distance: 90 - 91: 5.891 distance: 90 - 92: 3.563 distance: 93 - 94: 57.493 distance: 94 - 95: 57.215 distance: 94 - 97: 29.019 distance: 95 - 96: 41.086 distance: 95 - 102: 42.203 distance: 96 - 125: 35.477 distance: 97 - 98: 40.752 distance: 99 - 100: 47.053 distance: 99 - 101: 56.942 distance: 102 - 103: 44.174 distance: 103 - 104: 39.421 distance: 104 - 105: 43.373 distance: 104 - 110: 32.135 distance: 105 - 133: 28.570 distance: 107 - 109: 57.233