Starting phenix.real_space_refine on Tue Feb 11 00:32:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrj_32728/02_2025/7wrj_32728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrj_32728/02_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_32728/02_2025/7wrj_32728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrj_32728/02_2025/7wrj_32728.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrj_32728/02_2025/7wrj_32728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrj_32728/02_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-5592/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: 3.28, per 1000 atoms: 1.00 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: 0.76 Conformation dependent library (CDL) restraints added in 372.1 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: 0.38 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: 0.79 Time building geometry restraints manager: 0.89 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.920 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- 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 : 0.375 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: 0.1943 time to fit residues: 37.9812 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 : 0.468 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.134683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.116726 restraints weight = 8625.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120079 restraints weight = 5148.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.122462 restraints weight = 3501.331| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3373 Z= 0.275 Angle : 0.823 10.380 4593 Z= 0.424 Chirality : 0.049 0.194 512 Planarity : 0.008 0.126 588 Dihedral : 7.452 30.536 498 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.78 % Favored : 90.98 % 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: -2.74 (0.38), residues: 410 helix: -4.58 (0.88), residues: 12 sheet: -1.11 (0.42), residues: 123 loop : -2.15 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 49 HIS 0.005 0.002 HIS R 505 PHE 0.017 0.002 PHE R 377 TYR 0.016 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 : 0.380 Fit side-chains revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7446 (m-80) cc_final: 0.7216 (m-80) REVERT: R 428 ASP cc_start: 0.7664 (t0) cc_final: 0.7172 (t0) REVERT: R 496 SER cc_start: 0.8470 (t) cc_final: 0.7870 (p) REVERT: A 4 LEU cc_start: 0.9033 (mm) cc_final: 0.8806 (mm) REVERT: A 7 SER cc_start: 0.9328 (p) cc_final: 0.8997 (m) REVERT: A 61 TYR cc_start: 0.6299 (m-80) cc_final: 0.5921 (m-80) REVERT: A 62 ASN cc_start: 0.9051 (t0) cc_final: 0.8644 (t0) REVERT: A 111 ASP cc_start: 0.9106 (t0) cc_final: 0.8831 (t0) REVERT: A 115 MET cc_start: 0.8132 (tpt) cc_final: 0.7917 (tpp) REVERT: A 121 MET cc_start: 0.6896 (ptt) cc_final: 0.6683 (ppp) REVERT: B 36 TRP cc_start: 0.8169 (m100) cc_final: 0.7968 (m100) REVERT: B 91 THR cc_start: 0.8866 (m) cc_final: 0.8413 (p) REVERT: B 99 VAL cc_start: 0.9133 (t) cc_final: 0.8755 (t) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.1560 time to fit residues: 23.9069 Evaluate side-chains 96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.134788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.116962 restraints weight = 8424.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120193 restraints weight = 5007.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.122419 restraints weight = 3396.901| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3373 Z= 0.219 Angle : 0.730 7.000 4593 Z= 0.379 Chirality : 0.047 0.177 512 Planarity : 0.007 0.105 588 Dihedral : 6.770 31.264 498 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % 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: -2.53 (0.39), residues: 410 helix: -4.81 (0.64), residues: 14 sheet: -1.12 (0.43), residues: 132 loop : -1.86 (0.37), residues: 264 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 0.018 0.002 PHE R 377 TYR 0.020 0.002 TYR B 50 ARG 0.005 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 119 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7579 (m-80) cc_final: 0.7363 (m-80) REVERT: R 428 ASP cc_start: 0.7907 (t0) cc_final: 0.7267 (t0) REVERT: R 474 GLN cc_start: 0.6037 (OUTLIER) cc_final: 0.5523 (tm-30) REVERT: R 496 SER cc_start: 0.8426 (t) cc_final: 0.7918 (p) REVERT: A 4 LEU cc_start: 0.9103 (mm) cc_final: 0.8869 (mm) REVERT: A 61 TYR cc_start: 0.6357 (m-80) cc_final: 0.5822 (m-80) REVERT: A 62 ASN cc_start: 0.9057 (t0) cc_final: 0.8568 (t0) REVERT: A 111 ASP cc_start: 0.9044 (t0) cc_final: 0.8646 (t0) REVERT: A 115 MET cc_start: 0.8145 (tpt) cc_final: 0.7900 (tpp) REVERT: A 121 MET cc_start: 0.6886 (ptt) cc_final: 0.6592 (ppp) REVERT: B 99 VAL cc_start: 0.9100 (t) cc_final: 0.8689 (t) REVERT: B 106 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8501 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1412 time to fit residues: 20.7599 Evaluate side-chains 90 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.132816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114876 restraints weight = 8533.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.118072 restraints weight = 5027.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.120304 restraints weight = 3404.708| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4653 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= 0.235 Angle : 0.736 8.706 4593 Z= 0.372 Chirality : 0.047 0.199 512 Planarity : 0.007 0.110 588 Dihedral : 6.656 30.667 498 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -2.20 (0.41), residues: 410 helix: -4.88 (0.60), residues: 14 sheet: -0.99 (0.44), residues: 130 loop : -1.55 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 36 HIS 0.005 0.002 HIS A 99 PHE 0.025 0.002 PHE R 464 TYR 0.019 0.002 TYR B 50 ARG 0.004 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 121 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 428 ASP cc_start: 0.7917 (t0) cc_final: 0.7284 (t0) REVERT: A 61 TYR cc_start: 0.6755 (m-80) cc_final: 0.6029 (m-80) REVERT: A 62 ASN cc_start: 0.9008 (t0) cc_final: 0.8640 (t0) REVERT: A 111 ASP cc_start: 0.9107 (t0) cc_final: 0.8658 (t0) REVERT: A 121 MET cc_start: 0.7053 (ptt) cc_final: 0.6532 (ppp) REVERT: B 49 ILE cc_start: 0.8275 (tp) cc_final: 0.8067 (tp) REVERT: B 99 VAL cc_start: 0.9176 (t) cc_final: 0.8575 (t) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1385 time to fit residues: 20.5405 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 : 0.403 ------------------------------------------------------------------------------- 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: 0.7980 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 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 = 0.3870 r_free = 0.3870 target = 0.133063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115096 restraints weight = 8332.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118323 restraints weight = 4967.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.120657 restraints weight = 3381.094| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3373 Z= 0.221 Angle : 0.715 6.563 4593 Z= 0.369 Chirality : 0.047 0.181 512 Planarity : 0.006 0.092 588 Dihedral : 6.473 31.532 498 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -2.12 (0.42), residues: 410 helix: -4.80 (0.64), residues: 14 sheet: -1.02 (0.44), residues: 139 loop : -1.45 (0.40), residues: 257 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 0.002 PHE R 456 TYR 0.013 0.002 TYR R 423 ARG 0.005 0.001 ARG R 509 *********************** 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 123 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 402 ILE cc_start: 0.8828 (tt) cc_final: 0.8616 (tt) REVERT: R 428 ASP cc_start: 0.8019 (t0) cc_final: 0.7392 (t0) REVERT: A 13 LYS cc_start: 0.3908 (mmtt) cc_final: 0.3552 (mmmt) REVERT: A 61 TYR cc_start: 0.6788 (m-80) cc_final: 0.6516 (m-80) REVERT: A 121 MET cc_start: 0.7226 (ptt) cc_final: 0.6681 (ppp) REVERT: B 28 ASN cc_start: 0.7784 (p0) cc_final: 0.7561 (p0) REVERT: B 39 HIS cc_start: 0.7514 (t70) cc_final: 0.7259 (t70) REVERT: B 49 ILE cc_start: 0.8322 (tp) cc_final: 0.8084 (tp) REVERT: B 90 GLU cc_start: 0.7939 (pt0) cc_final: 0.7708 (pt0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1423 time to fit residues: 21.4002 Evaluate side-chains 90 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 10.0000 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 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 = 0.3804 r_free = 0.3804 target = 0.128953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110907 restraints weight = 8573.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114122 restraints weight = 5123.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116319 restraints weight = 3472.961| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3373 Z= 0.292 Angle : 0.749 8.999 4593 Z= 0.388 Chirality : 0.047 0.176 512 Planarity : 0.007 0.118 588 Dihedral : 6.843 35.662 498 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -2.04 (0.42), residues: 410 helix: -3.91 (0.78), residues: 20 sheet: -0.97 (0.45), residues: 139 loop : -1.36 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 49 HIS 0.007 0.002 HIS R 505 PHE 0.020 0.002 PHE R 377 TYR 0.018 0.002 TYR R 423 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 119 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7879 (m-80) cc_final: 0.7428 (m-80) REVERT: R 386 LYS cc_start: 0.8031 (pttt) cc_final: 0.7639 (pttp) REVERT: R 428 ASP cc_start: 0.8146 (t0) cc_final: 0.7670 (t70) REVERT: R 496 SER cc_start: 0.8459 (p) cc_final: 0.8174 (p) REVERT: A 40 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8101 (ttm-80) REVERT: A 49 TRP cc_start: 0.8333 (t60) cc_final: 0.8078 (t60) REVERT: A 121 MET cc_start: 0.7503 (ptt) cc_final: 0.6869 (ppp) REVERT: B 49 ILE cc_start: 0.8628 (tp) cc_final: 0.8383 (tp) REVERT: B 52 ASN cc_start: 0.6414 (m-40) cc_final: 0.6170 (m-40) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1562 time to fit residues: 22.6937 Evaluate side-chains 92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 0.6980 chunk 28 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.131689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113779 restraints weight = 8332.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116930 restraints weight = 4995.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119182 restraints weight = 3402.360| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3373 Z= 0.203 Angle : 0.720 6.863 4593 Z= 0.368 Chirality : 0.046 0.187 512 Planarity : 0.007 0.099 588 Dihedral : 6.545 34.844 498 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % 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: -2.02 (0.42), residues: 410 helix: -3.64 (0.92), residues: 20 sheet: -0.96 (0.45), residues: 139 loop : -1.37 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 36 HIS 0.005 0.002 HIS A 99 PHE 0.019 0.002 PHE R 377 TYR 0.023 0.002 TYR A 61 ARG 0.004 0.001 ARG A 40 *********************** 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 131 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: R 386 LYS cc_start: 0.7906 (pttt) cc_final: 0.7557 (pttp) REVERT: R 428 ASP cc_start: 0.8100 (t0) cc_final: 0.7601 (t70) REVERT: R 496 SER cc_start: 0.8489 (p) cc_final: 0.8167 (p) REVERT: R 500 THR cc_start: 0.8814 (p) cc_final: 0.8365 (t) REVERT: A 13 LYS cc_start: 0.4291 (mmtt) cc_final: 0.3941 (mmmt) REVERT: A 40 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.7983 (ttm-80) REVERT: A 62 ASN cc_start: 0.8876 (t0) cc_final: 0.8433 (t0) REVERT: A 121 MET cc_start: 0.7442 (ptt) cc_final: 0.6875 (ppp) REVERT: B 49 ILE cc_start: 0.8201 (tp) cc_final: 0.7970 (tp) REVERT: B 89 CYS cc_start: 0.6346 (p) cc_final: 0.6025 (p) REVERT: B 93 ASP cc_start: 0.7260 (t0) cc_final: 0.6875 (t0) REVERT: B 99 VAL cc_start: 0.9176 (t) cc_final: 0.8836 (t) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1424 time to fit residues: 22.7537 Evaluate side-chains 98 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 38 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 417 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.131437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113609 restraints weight = 8408.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116926 restraints weight = 4949.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119267 restraints weight = 3302.985| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3373 Z= 0.248 Angle : 0.729 6.512 4593 Z= 0.378 Chirality : 0.047 0.181 512 Planarity : 0.006 0.091 588 Dihedral : 6.723 36.565 498 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % 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 : 0.00 % 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: -2.04 (0.42), residues: 410 helix: -3.73 (0.81), residues: 20 sheet: -0.93 (0.46), residues: 139 loop : -1.41 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP A 49 HIS 0.005 0.001 HIS A 99 PHE 0.029 0.002 PHE R 377 TYR 0.019 0.002 TYR B 37 ARG 0.005 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 128 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.8032 (pttt) cc_final: 0.7669 (pttp) REVERT: R 428 ASP cc_start: 0.8181 (t0) cc_final: 0.7713 (t70) REVERT: R 455 LEU cc_start: 0.8045 (mt) cc_final: 0.7829 (mm) REVERT: R 500 THR cc_start: 0.8842 (p) cc_final: 0.8352 (t) REVERT: A 13 LYS cc_start: 0.4556 (mmtt) cc_final: 0.3854 (mmmt) REVERT: A 15 LYS cc_start: 0.8590 (tppt) cc_final: 0.7841 (tmmt) REVERT: A 40 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: A 61 TYR cc_start: 0.6200 (m-80) cc_final: 0.5939 (m-80) REVERT: A 62 ASN cc_start: 0.8919 (t0) cc_final: 0.8386 (t0) REVERT: A 86 ASN cc_start: 0.8154 (m-40) cc_final: 0.7662 (m-40) REVERT: A 121 MET cc_start: 0.7317 (ptt) cc_final: 0.6875 (ppp) REVERT: B 93 ASP cc_start: 0.7315 (t0) cc_final: 0.7012 (t0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1449 time to fit residues: 22.7142 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 : 0.364 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3804 r_free = 0.3804 target = 0.128063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110039 restraints weight = 8608.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.113250 restraints weight = 5084.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.115563 restraints weight = 3467.143| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3373 Z= 0.273 Angle : 0.773 11.128 4593 Z= 0.392 Chirality : 0.047 0.193 512 Planarity : 0.006 0.088 588 Dihedral : 6.900 37.274 498 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.54 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -3.85 (0.70), residues: 26 sheet: -0.86 (0.47), residues: 139 loop : -1.45 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 36 HIS 0.009 0.003 HIS B 51 PHE 0.016 0.002 PHE R 377 TYR 0.018 0.002 TYR B 37 ARG 0.005 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 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: symmetry clash revert: symmetry clash REVERT: R 405 ASP cc_start: 0.8846 (t0) cc_final: 0.8627 (t0) REVERT: R 428 ASP cc_start: 0.8183 (t0) cc_final: 0.7730 (t70) REVERT: R 500 THR cc_start: 0.8884 (p) cc_final: 0.8381 (t) REVERT: A 13 LYS cc_start: 0.4736 (mmtt) cc_final: 0.3997 (mmmt) REVERT: A 49 TRP cc_start: 0.8421 (t60) cc_final: 0.8214 (t60) REVERT: A 96 PHE cc_start: 0.9190 (m-80) cc_final: 0.8978 (m-10) REVERT: A 121 MET cc_start: 0.7539 (ptt) cc_final: 0.6934 (ppp) REVERT: B 52 ASN cc_start: 0.7089 (m-40) cc_final: 0.6029 (m-40) REVERT: B 89 CYS cc_start: 0.6605 (p) cc_final: 0.6362 (p) REVERT: B 93 ASP cc_start: 0.7351 (t0) cc_final: 0.6939 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1506 time to fit residues: 22.1324 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 : 0.366 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.127655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110087 restraints weight = 8452.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113299 restraints weight = 4967.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115471 restraints weight = 3359.975| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 3373 Z= 0.286 Angle : 0.762 8.807 4593 Z= 0.390 Chirality : 0.048 0.176 512 Planarity : 0.006 0.087 588 Dihedral : 6.925 37.682 498 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % 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 : 0.00 % 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: -2.15 (0.41), residues: 410 helix: -3.86 (0.69), residues: 26 sheet: -0.81 (0.46), residues: 140 loop : -1.54 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 116 HIS 0.004 0.002 HIS A 99 PHE 0.025 0.002 PHE R 377 TYR 0.026 0.002 TYR B 50 ARG 0.005 0.001 ARG R 454 ********************** 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 126 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 428 ASP cc_start: 0.8167 (t0) cc_final: 0.7709 (t70) REVERT: R 498 ARG cc_start: 0.8310 (ptp-170) cc_final: 0.7842 (ptp-170) REVERT: A 1 GLN cc_start: 0.6709 (pm20) cc_final: 0.6493 (pm20) REVERT: A 13 LYS cc_start: 0.4597 (mmtt) cc_final: 0.3893 (mmmt) REVERT: A 15 LYS cc_start: 0.8695 (tppt) cc_final: 0.7888 (tmmt) REVERT: A 61 TYR cc_start: 0.6333 (m-80) cc_final: 0.6095 (m-80) REVERT: A 62 ASN cc_start: 0.8902 (t0) cc_final: 0.8356 (t0) REVERT: A 96 PHE cc_start: 0.9233 (m-80) cc_final: 0.8504 (m-10) REVERT: A 97 CYS cc_start: 0.5142 (p) cc_final: 0.4859 (p) REVERT: A 121 MET cc_start: 0.7554 (ptt) cc_final: 0.7027 (ppp) REVERT: B 52 ASN cc_start: 0.7311 (m-40) cc_final: 0.6675 (m-40) REVERT: B 86 ASP cc_start: 0.6870 (m-30) cc_final: 0.6651 (m-30) REVERT: B 106 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.7935 (mtp85) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1508 time to fit residues: 23.0586 Evaluate side-chains 103 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 R 474 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111959 restraints weight = 8443.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115202 restraints weight = 4989.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.117499 restraints weight = 3415.008| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3373 Z= 0.222 Angle : 0.726 7.639 4593 Z= 0.367 Chirality : 0.047 0.182 512 Planarity : 0.006 0.085 588 Dihedral : 6.679 37.407 498 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.27 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -2.07 (0.41), residues: 410 helix: -3.90 (0.71), residues: 26 sheet: -0.78 (0.46), residues: 140 loop : -1.45 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 36 HIS 0.006 0.002 HIS B 51 PHE 0.016 0.002 PHE R 486 TYR 0.014 0.002 TYR B 37 ARG 0.005 0.001 ARG A 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.64 seconds wall clock time: 31 minutes 7.82 seconds (1867.82 seconds total)