Starting phenix.real_space_refine on Wed Mar 5 19:34:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrj_32728/03_2025/7wrj_32728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrj_32728/03_2025/7wrj_32728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrj_32728/03_2025/7wrj_32728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrj_32728/03_2025/7wrj_32728.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrj_32728/03_2025/7wrj_32728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrj_32728/03_2025/7wrj_32728.cif" } resolution = 4.08 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 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= 0.014 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 14 5.16 5 C 2091 2.51 5 N 557 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3289 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 973 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 784 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.06, per 1000 atoms: 0.93 Number of scatterers: 3289 At special positions: 0 Unit cell: (73.83, 75.97, 85.6, 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 14 16.00 O 627 8.00 N 557 7.00 C 2091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 407.2 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 403 through 407 removed outlier: 3.704A pdb=" N VAL R 407 " --> pdb=" O GLY R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 502 through 506 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.954A pdb=" N ASP B 83 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU B 84 " --> pdb=" O SER B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.628A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL R 512 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.510A pdb=" N THR A 83 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.589A pdb=" N ALA A 98 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 36 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 52 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP A 38 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 52 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 60 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.868A pdb=" N MET A 115 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 10 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 5.736A pdb=" N LEU B 47 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 90 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 98 " --> pdb=" O ASP B 93 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 174 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: 0.82 Time building geometry restraints manager: 1.09 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: 997 1.33 - 1.46: 912 1.46 - 1.59: 1448 1.59 - 1.72: 1 1.72 - 1.85: 15 Bond restraints: 3373 Sorted by residual: bond pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.73e+00 bond pdb=" CG1 ILE R 418 " pdb=" CD1 ILE R 418 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.27e+00 bond pdb=" C PRO R 373 " pdb=" O PRO R 373 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.30e-02 5.92e+03 5.12e+00 bond pdb=" CA CYS R 525 " pdb=" C CYS R 525 " ideal model delta sigma weight residual 1.527 1.548 -0.021 9.80e-03 1.04e+04 4.56e+00 bond pdb=" N LEU R 371 " pdb=" CA LEU R 371 " ideal model delta sigma weight residual 1.464 1.489 -0.025 1.20e-02 6.94e+03 4.33e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 4250 2.26 - 4.52: 276 4.52 - 6.78: 51 6.78 - 9.04: 10 9.04 - 11.30: 6 Bond angle restraints: 4593 Sorted by residual: angle pdb=" N PRO R 373 " pdb=" CA PRO R 373 " pdb=" CB PRO R 373 " ideal model delta sigma weight residual 103.25 96.66 6.59 1.05e+00 9.07e-01 3.94e+01 angle pdb=" N ASN R 370 " pdb=" CA ASN R 370 " pdb=" C ASN R 370 " ideal model delta sigma weight residual 113.16 106.83 6.33 1.24e+00 6.50e-01 2.61e+01 angle pdb=" C ASP R 364 " pdb=" N TYR R 365 " pdb=" CA TYR R 365 " ideal model delta sigma weight residual 120.28 127.60 -7.32 1.44e+00 4.82e-01 2.58e+01 angle pdb=" C TYR B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.33e+01 angle pdb=" CB GLN R 409 " pdb=" CG GLN R 409 " pdb=" CD GLN R 409 " ideal model delta sigma weight residual 112.60 119.86 -7.26 1.70e+00 3.46e-01 1.82e+01 ... (remaining 4588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 1701 14.56 - 29.12: 247 29.12 - 43.68: 52 43.68 - 58.24: 10 58.24 - 72.80: 5 Dihedral angle restraints: 2015 sinusoidal: 811 harmonic: 1204 Sorted by residual: dihedral pdb=" CA LEU R 461 " pdb=" C LEU R 461 " pdb=" N LYS R 462 " pdb=" CA LYS R 462 " ideal model delta harmonic sigma weight residual 180.00 148.97 31.03 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLN B 80 " pdb=" C GLN B 80 " pdb=" N SER B 81 " pdb=" CA SER B 81 " ideal model delta harmonic sigma weight residual -180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual -86.00 -131.11 45.11 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 320 0.059 - 0.118: 145 0.118 - 0.177: 39 0.177 - 0.235: 6 0.235 - 0.294: 2 Chirality restraints: 512 Sorted by residual: chirality pdb=" CB ILE R 468 " pdb=" CA ILE R 468 " pdb=" CG1 ILE R 468 " pdb=" CG2 ILE R 468 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CG LEU B 96 " pdb=" CB LEU B 96 " pdb=" CD1 LEU B 96 " pdb=" CD2 LEU B 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU B 48 " pdb=" CB LEU B 48 " pdb=" CD1 LEU B 48 " pdb=" CD2 LEU B 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 509 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 365 " 0.013 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR R 365 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR R 365 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR R 365 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR R 365 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 365 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 365 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 365 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 369 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C TYR R 369 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 369 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN R 370 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.017 2.00e-02 2.50e+03 2.05e-02 8.38e+00 pdb=" CG TYR B 88 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.000 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 824 2.78 - 3.31: 3092 3.31 - 3.84: 5780 3.84 - 4.37: 6424 4.37 - 4.90: 10952 Nonbonded interactions: 27072 Sorted by model distance: nonbonded pdb=" OG SER R 438 " pdb=" O LYS R 440 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR B 13 " pdb=" OE1 GLN B 16 " model vdw 2.260 3.040 nonbonded pdb=" O PRO B 7 " pdb=" OG1 THR B 105 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.304 3.040 nonbonded pdb=" O TYR R 396 " pdb=" OG SER R 514 " model vdw 2.307 3.040 ... (remaining 27067 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.009 0.105 3373 Z= 0.578 Angle : 1.316 11.297 4593 Z= 0.709 Chirality : 0.069 0.294 512 Planarity : 0.009 0.067 588 Dihedral : 14.006 72.801 1232 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.73 % Allowed : 11.46 % Favored : 87.80 % Rotamer: Outliers : 0.55 % Allowed : 1.38 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.57 (0.39), residues: 410 helix: -4.65 (0.52), residues: 21 sheet: -0.77 (0.43), residues: 142 loop : -2.08 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 55 HIS 0.011 0.003 HIS R 505 PHE 0.034 0.004 PHE A 96 TYR 0.066 0.005 TYR R 365 ARG 0.013 0.002 ARG R 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: R 353 TRP cc_start: 0.8506 (p-90) cc_final: 0.7034 (p-90) REVERT: R 387 LEU cc_start: 0.8124 (mp) cc_final: 0.7594 (mp) REVERT: R 396 TYR cc_start: 0.6913 (m-80) cc_final: 0.6704 (m-80) REVERT: R 410 ILE cc_start: 0.8475 (mm) cc_final: 0.8256 (mm) REVERT: R 453 TYR cc_start: 0.7520 (p90) cc_final: 0.7297 (p90) REVERT: R 496 SER cc_start: 0.8448 (t) cc_final: 0.8174 (p) REVERT: A 4 LEU cc_start: 0.8974 (mm) cc_final: 0.8682 (mm) REVERT: A 7 SER cc_start: 0.9348 (p) cc_final: 0.8987 (m) REVERT: A 69 LEU cc_start: 0.8035 (mm) cc_final: 0.7822 (mm) REVERT: A 115 MET cc_start: 0.8302 (tpt) cc_final: 0.7835 (tpp) REVERT: A 121 MET cc_start: 0.6637 (ptt) cc_final: 0.6414 (ppp) REVERT: B 36 TRP cc_start: 0.8302 (m100) cc_final: 0.8068 (m100) REVERT: B 37 TYR cc_start: 0.7704 (m-80) cc_final: 0.7322 (m-80) REVERT: B 90 GLU cc_start: 0.8174 (pt0) cc_final: 0.6755 (pt0) REVERT: B 91 THR cc_start: 0.8922 (m) cc_final: 0.8603 (p) REVERT: B 101 PHE cc_start: 0.8501 (m-80) cc_final: 0.8251 (m-10) REVERT: B 109 VAL cc_start: 0.3809 (p) cc_final: 0.3388 (p) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.2268 time to fit residues: 44.4964 Evaluate side-chains 102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 38 GLN B 39 HIS ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.133965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116149 restraints weight = 8634.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119445 restraints weight = 5164.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121773 restraints weight = 3502.433| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3373 Z= 0.272 Angle : 0.824 9.336 4593 Z= 0.425 Chirality : 0.049 0.212 512 Planarity : 0.008 0.123 588 Dihedral : 7.452 30.580 498 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.27 % Favored : 90.49 % Rotamer: Outliers : 0.28 % Allowed : 7.46 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.75 (0.38), residues: 410 helix: -4.57 (0.89), residues: 12 sheet: -1.10 (0.42), residues: 123 loop : -2.17 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 49 HIS 0.006 0.002 HIS A 99 PHE 0.016 0.002 PHE R 377 TYR 0.017 0.002 TYR R 421 ARG 0.006 0.001 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7479 (m-80) cc_final: 0.7206 (m-80) REVERT: R 428 ASP cc_start: 0.7736 (t0) cc_final: 0.7200 (t0) REVERT: R 496 SER cc_start: 0.8471 (t) cc_final: 0.7875 (p) REVERT: A 4 LEU cc_start: 0.9056 (mm) cc_final: 0.8824 (mm) REVERT: A 7 SER cc_start: 0.9329 (p) cc_final: 0.9007 (m) REVERT: A 61 TYR cc_start: 0.6337 (m-80) cc_final: 0.5955 (m-80) REVERT: A 62 ASN cc_start: 0.9065 (t0) cc_final: 0.8650 (t0) REVERT: A 111 ASP cc_start: 0.9104 (t0) cc_final: 0.8829 (t0) REVERT: A 115 MET cc_start: 0.8177 (tpt) cc_final: 0.7956 (tpp) REVERT: A 121 MET cc_start: 0.6903 (ptt) cc_final: 0.6646 (ppp) REVERT: B 36 TRP cc_start: 0.8174 (m100) cc_final: 0.7973 (m100) REVERT: B 91 THR cc_start: 0.8871 (m) cc_final: 0.8423 (p) REVERT: B 99 VAL cc_start: 0.9129 (t) cc_final: 0.8768 (t) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.1522 time to fit residues: 23.1091 Evaluate side-chains 97 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.0010 chunk 37 optimal weight: 0.0030 chunk 0 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN R 474 GLN B 6 GLN B 38 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.135587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.117669 restraints weight = 8436.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120878 restraints weight = 5004.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.123118 restraints weight = 3413.004| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3373 Z= 0.209 Angle : 0.731 6.954 4593 Z= 0.379 Chirality : 0.047 0.178 512 Planarity : 0.007 0.104 588 Dihedral : 6.785 31.197 498 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.28 % Allowed : 5.25 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.60 (0.39), residues: 410 helix: -4.81 (0.63), residues: 14 sheet: -1.12 (0.43), residues: 126 loop : -1.94 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 49 HIS 0.005 0.002 HIS A 99 PHE 0.017 0.001 PHE R 377 TYR 0.021 0.002 TYR B 50 ARG 0.004 0.001 ARG R 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7573 (m-80) cc_final: 0.7364 (m-80) REVERT: R 428 ASP cc_start: 0.7975 (t0) cc_final: 0.7332 (t0) REVERT: R 474 GLN cc_start: 0.5961 (OUTLIER) cc_final: 0.5425 (tm-30) REVERT: R 496 SER cc_start: 0.8418 (t) cc_final: 0.7943 (p) REVERT: A 4 LEU cc_start: 0.9095 (mm) cc_final: 0.8859 (mm) REVERT: A 41 GLN cc_start: 0.8886 (tp40) cc_final: 0.8614 (tp40) REVERT: A 61 TYR cc_start: 0.6409 (m-80) cc_final: 0.5822 (m-80) REVERT: A 62 ASN cc_start: 0.9064 (t0) cc_final: 0.8592 (t0) REVERT: A 111 ASP cc_start: 0.9038 (t0) cc_final: 0.8671 (t0) REVERT: A 115 MET cc_start: 0.8136 (tpt) cc_final: 0.7899 (tpp) REVERT: A 121 MET cc_start: 0.6882 (ptt) cc_final: 0.6618 (ppp) REVERT: B 99 VAL cc_start: 0.9093 (t) cc_final: 0.8761 (t) REVERT: B 106 ARG cc_start: 0.8774 (mtm110) cc_final: 0.8463 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1340 time to fit residues: 19.7592 Evaluate side-chains 92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.128998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110769 restraints weight = 8712.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113808 restraints weight = 5305.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.116056 restraints weight = 3680.155| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3373 Z= 0.356 Angle : 0.818 8.902 4593 Z= 0.422 Chirality : 0.049 0.193 512 Planarity : 0.007 0.110 588 Dihedral : 7.195 33.891 498 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.20 (0.41), residues: 410 helix: -4.89 (0.58), residues: 14 sheet: -0.98 (0.44), residues: 132 loop : -1.56 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP B 36 HIS 0.006 0.003 HIS R 505 PHE 0.020 0.003 PHE R 338 TYR 0.020 0.002 TYR B 50 ARG 0.005 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.351 Fit side-chains REVERT: R 365 TYR cc_start: 0.7804 (m-80) cc_final: 0.7478 (m-80) REVERT: R 402 ILE cc_start: 0.8944 (tt) cc_final: 0.8702 (tt) REVERT: R 428 ASP cc_start: 0.8099 (t0) cc_final: 0.7542 (t0) REVERT: A 40 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8001 (ttm-80) REVERT: A 49 TRP cc_start: 0.8167 (t60) cc_final: 0.7939 (t60) REVERT: A 61 TYR cc_start: 0.6966 (m-80) cc_final: 0.6739 (m-80) REVERT: A 97 CYS cc_start: 0.5119 (p) cc_final: 0.4909 (p) REVERT: A 108 ILE cc_start: 0.8807 (mp) cc_final: 0.8572 (mp) REVERT: A 121 MET cc_start: 0.7475 (ptt) cc_final: 0.6841 (ppp) REVERT: B 37 TYR cc_start: 0.7758 (m-10) cc_final: 0.6330 (m-10) REVERT: B 49 ILE cc_start: 0.8569 (tp) cc_final: 0.8318 (tp) REVERT: B 106 ARG cc_start: 0.8725 (mtm110) cc_final: 0.8476 (mtp85) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1429 time to fit residues: 20.8020 Evaluate side-chains 89 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 417 ASN B 6 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.128823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111182 restraints weight = 8425.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114239 restraints weight = 5061.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116478 restraints weight = 3469.618| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3373 Z= 0.293 Angle : 0.754 8.006 4593 Z= 0.390 Chirality : 0.048 0.172 512 Planarity : 0.007 0.094 588 Dihedral : 6.870 34.117 498 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.28 % Allowed : 4.42 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.21 (0.42), residues: 410 helix: -4.81 (0.64), residues: 14 sheet: -1.10 (0.44), residues: 141 loop : -1.50 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 36 HIS 0.005 0.002 HIS R 505 PHE 0.018 0.002 PHE R 456 TYR 0.018 0.002 TYR B 50 ARG 0.006 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.8024 (pttt) cc_final: 0.7609 (pttp) REVERT: R 428 ASP cc_start: 0.8149 (t0) cc_final: 0.7587 (t0) REVERT: R 500 THR cc_start: 0.8869 (p) cc_final: 0.8366 (t) REVERT: A 40 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.7877 (ttm-80) REVERT: A 49 TRP cc_start: 0.8339 (t60) cc_final: 0.8075 (t60) REVERT: A 121 MET cc_start: 0.7537 (ptt) cc_final: 0.6901 (ppp) REVERT: B 49 ILE cc_start: 0.8480 (tp) cc_final: 0.8224 (tp) REVERT: B 52 ASN cc_start: 0.6588 (m-40) cc_final: 0.6339 (m-40) REVERT: B 89 CYS cc_start: 0.6458 (p) cc_final: 0.6168 (p) REVERT: B 106 ARG cc_start: 0.8686 (mtm110) cc_final: 0.8303 (mtp85) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1385 time to fit residues: 20.5086 Evaluate side-chains 93 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 39 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.131189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113542 restraints weight = 8445.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.116760 restraints weight = 5083.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119031 restraints weight = 3438.065| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3373 Z= 0.221 Angle : 0.730 9.060 4593 Z= 0.374 Chirality : 0.046 0.203 512 Planarity : 0.007 0.119 588 Dihedral : 6.651 35.196 498 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.73 % Rotamer: Outliers : 0.28 % Allowed : 2.76 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.10 (0.42), residues: 410 helix: -3.79 (0.86), residues: 20 sheet: -1.00 (0.45), residues: 141 loop : -1.42 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 38 HIS 0.005 0.002 HIS A 99 PHE 0.017 0.002 PHE R 377 TYR 0.018 0.002 TYR R 421 ARG 0.004 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7946 (pttt) cc_final: 0.7537 (pttp) REVERT: R 428 ASP cc_start: 0.8150 (t0) cc_final: 0.7554 (t0) REVERT: R 500 THR cc_start: 0.8910 (p) cc_final: 0.8427 (t) REVERT: A 96 PHE cc_start: 0.9199 (m-80) cc_final: 0.8472 (m-10) REVERT: A 121 MET cc_start: 0.7529 (ptt) cc_final: 0.6863 (ppp) REVERT: B 49 ILE cc_start: 0.8627 (tp) cc_final: 0.8408 (tp) REVERT: B 52 ASN cc_start: 0.6358 (m-40) cc_final: 0.6052 (m-40) REVERT: B 89 CYS cc_start: 0.6141 (p) cc_final: 0.5744 (p) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.1298 time to fit residues: 19.6911 Evaluate side-chains 94 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN R 417 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112443 restraints weight = 8288.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115739 restraints weight = 4907.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118030 restraints weight = 3290.393| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3373 Z= 0.255 Angle : 0.754 10.408 4593 Z= 0.386 Chirality : 0.047 0.190 512 Planarity : 0.007 0.101 588 Dihedral : 6.673 36.317 498 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.14 (0.41), residues: 410 helix: -3.89 (0.81), residues: 20 sheet: -0.97 (0.46), residues: 139 loop : -1.49 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 36 HIS 0.004 0.002 HIS A 99 PHE 0.014 0.002 PHE R 377 TYR 0.021 0.002 TYR B 50 ARG 0.005 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.8174 (pttt) cc_final: 0.7807 (pttp) REVERT: R 428 ASP cc_start: 0.8170 (t0) cc_final: 0.7694 (t70) REVERT: A 40 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8100 (ttm-80) REVERT: A 49 TRP cc_start: 0.8519 (t60) cc_final: 0.8091 (t60) REVERT: A 86 ASN cc_start: 0.8189 (m-40) cc_final: 0.7824 (t0) REVERT: A 96 PHE cc_start: 0.9213 (m-80) cc_final: 0.8447 (m-10) REVERT: A 121 MET cc_start: 0.7543 (ptt) cc_final: 0.7073 (ppp) REVERT: B 52 ASN cc_start: 0.6492 (m-40) cc_final: 0.6138 (m-40) REVERT: B 89 CYS cc_start: 0.6598 (p) cc_final: 0.6203 (p) REVERT: B 93 ASP cc_start: 0.7422 (t0) cc_final: 0.7002 (t0) REVERT: B 106 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8178 (mtp85) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1433 time to fit residues: 21.1457 Evaluate side-chains 100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 0.0000 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108559 restraints weight = 8549.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111591 restraints weight = 5200.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113572 restraints weight = 3589.647| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3373 Z= 0.341 Angle : 0.797 8.130 4593 Z= 0.412 Chirality : 0.049 0.175 512 Planarity : 0.007 0.094 588 Dihedral : 7.083 38.069 498 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.49 % Favored : 89.27 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.14 (0.42), residues: 410 helix: -3.99 (0.83), residues: 20 sheet: -1.04 (0.46), residues: 140 loop : -1.43 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 116 HIS 0.004 0.002 HIS R 505 PHE 0.023 0.002 PHE R 377 TYR 0.019 0.002 TYR R 421 ARG 0.008 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: R 365 TYR cc_start: 0.8146 (m-80) cc_final: 0.7931 (m-80) REVERT: R 386 LYS cc_start: 0.8233 (pttt) cc_final: 0.7988 (pttp) REVERT: R 428 ASP cc_start: 0.8252 (t0) cc_final: 0.7811 (t70) REVERT: A 40 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8075 (ttm-80) REVERT: A 49 TRP cc_start: 0.8559 (t60) cc_final: 0.8157 (t60) REVERT: A 86 ASN cc_start: 0.8235 (m-40) cc_final: 0.7990 (m-40) REVERT: A 97 CYS cc_start: 0.4995 (p) cc_final: 0.4766 (p) REVERT: A 121 MET cc_start: 0.7639 (ptt) cc_final: 0.7208 (ppp) REVERT: B 36 TRP cc_start: 0.8528 (m100) cc_final: 0.8269 (m100) REVERT: B 52 ASN cc_start: 0.7430 (m-40) cc_final: 0.6930 (m-40) REVERT: B 89 CYS cc_start: 0.6171 (p) cc_final: 0.5643 (p) REVERT: B 93 ASP cc_start: 0.7500 (t0) cc_final: 0.7046 (t0) REVERT: B 106 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8290 (mtp85) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1303 time to fit residues: 18.4855 Evaluate side-chains 95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 0.0470 chunk 17 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 417 ASN R 474 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.129014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111448 restraints weight = 8544.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114733 restraints weight = 5015.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.116966 restraints weight = 3387.646| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3373 Z= 0.226 Angle : 0.764 6.029 4593 Z= 0.393 Chirality : 0.047 0.181 512 Planarity : 0.006 0.090 588 Dihedral : 6.827 37.994 498 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.41), residues: 410 helix: -3.90 (0.83), residues: 20 sheet: -1.00 (0.47), residues: 139 loop : -1.48 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 36 HIS 0.004 0.002 HIS A 99 PHE 0.016 0.002 PHE R 377 TYR 0.029 0.002 TYR B 50 ARG 0.007 0.001 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: R 406 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8314 (mm-30) REVERT: R 428 ASP cc_start: 0.8092 (t0) cc_final: 0.7703 (t70) REVERT: A 40 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8176 (ttm-80) REVERT: A 49 TRP cc_start: 0.8526 (t60) cc_final: 0.8144 (t60) REVERT: A 96 PHE cc_start: 0.9144 (m-80) cc_final: 0.8417 (m-10) REVERT: A 121 MET cc_start: 0.7493 (ptt) cc_final: 0.7094 (ppp) REVERT: B 36 TRP cc_start: 0.8446 (m100) cc_final: 0.8183 (m100) REVERT: B 52 ASN cc_start: 0.7388 (m-40) cc_final: 0.6805 (m-40) REVERT: B 89 CYS cc_start: 0.6218 (p) cc_final: 0.5106 (p) REVERT: B 93 ASP cc_start: 0.7449 (t0) cc_final: 0.6997 (t0) REVERT: B 106 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8422 (mtp85) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1380 time to fit residues: 20.1808 Evaluate side-chains 97 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.2980 chunk 33 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113640 restraints weight = 8624.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.116844 restraints weight = 5170.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.119106 restraints weight = 3564.046| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 3373 Z= 0.215 Angle : 0.782 10.731 4593 Z= 0.395 Chirality : 0.048 0.182 512 Planarity : 0.006 0.087 588 Dihedral : 6.717 38.164 498 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.24 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.15 (0.41), residues: 410 helix: -3.90 (0.82), residues: 20 sheet: -1.02 (0.45), residues: 141 loop : -1.47 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 36 HIS 0.004 0.002 HIS B 51 PHE 0.024 0.002 PHE R 377 TYR 0.012 0.001 TYR B 50 ARG 0.004 0.001 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: R 405 ASP cc_start: 0.9044 (t0) cc_final: 0.8826 (t0) REVERT: R 406 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8219 (mm-30) REVERT: R 409 GLN cc_start: 0.9080 (mm110) cc_final: 0.8258 (mm-40) REVERT: R 428 ASP cc_start: 0.8110 (t0) cc_final: 0.7661 (t70) REVERT: R 500 THR cc_start: 0.8598 (p) cc_final: 0.8016 (t) REVERT: A 40 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8194 (ttm-80) REVERT: A 49 TRP cc_start: 0.8431 (t60) cc_final: 0.8021 (t60) REVERT: A 96 PHE cc_start: 0.9051 (m-80) cc_final: 0.8341 (m-10) REVERT: A 115 MET cc_start: 0.7763 (tpp) cc_final: 0.7401 (ttm) REVERT: A 121 MET cc_start: 0.7375 (ptt) cc_final: 0.7014 (ppp) REVERT: B 36 TRP cc_start: 0.8476 (m100) cc_final: 0.8226 (m100) REVERT: B 89 CYS cc_start: 0.5807 (p) cc_final: 0.5146 (p) REVERT: B 93 ASP cc_start: 0.7391 (t0) cc_final: 0.6813 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1444 time to fit residues: 21.5977 Evaluate side-chains 99 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.130360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112042 restraints weight = 8566.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115245 restraints weight = 5168.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117519 restraints weight = 3544.580| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3373 Z= 0.243 Angle : 0.781 8.697 4593 Z= 0.392 Chirality : 0.047 0.180 512 Planarity : 0.006 0.086 588 Dihedral : 6.710 38.440 498 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.24 % Favored : 89.51 % Rotamer: Outliers : 0.28 % Allowed : 0.55 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.11 (0.42), residues: 410 helix: -4.08 (0.66), residues: 26 sheet: -0.83 (0.47), residues: 136 loop : -1.44 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 55 HIS 0.005 0.002 HIS B 51 PHE 0.013 0.002 PHE R 377 TYR 0.013 0.002 TYR R 423 ARG 0.005 0.001 ARG B 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.43 seconds wall clock time: 31 minutes 11.98 seconds (1871.98 seconds total)