Starting phenix.real_space_refine on Fri Dec 27 07:34:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrj_32728/12_2024/7wrj_32728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrj_32728/12_2024/7wrj_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_32728/12_2024/7wrj_32728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrj_32728/12_2024/7wrj_32728.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrj_32728/12_2024/7wrj_32728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrj_32728/12_2024/7wrj_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-5532/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: 3.46, per 1000 atoms: 1.05 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: 0.94 Conformation dependent library (CDL) restraints added in 710.1 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: 0.44 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: 0.90 Time building geometry restraints manager: 1.03 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: 2.950 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- 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 : 0.429 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: 0.1997 time to fit residues: 39.2964 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 : 0.399 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.479 Fit side-chains revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7659 (m-80) cc_final: 0.7374 (m-80) REVERT: R 428 ASP cc_start: 0.7873 (t0) cc_final: 0.7390 (t0) REVERT: R 496 SER cc_start: 0.8467 (t) cc_final: 0.7873 (p) REVERT: A 4 LEU cc_start: 0.9117 (mm) cc_final: 0.8827 (mm) REVERT: A 7 SER cc_start: 0.9208 (p) cc_final: 0.8916 (m) REVERT: A 61 TYR cc_start: 0.6159 (m-80) cc_final: 0.5772 (m-80) REVERT: A 62 ASN cc_start: 0.9040 (t0) cc_final: 0.8612 (t0) REVERT: A 111 ASP cc_start: 0.9109 (t0) cc_final: 0.8830 (t0) REVERT: A 115 MET cc_start: 0.8421 (tpt) cc_final: 0.8146 (tpp) REVERT: A 121 MET cc_start: 0.7092 (ptt) cc_final: 0.6705 (ppp) REVERT: B 36 TRP cc_start: 0.8256 (m100) cc_final: 0.7952 (m100) REVERT: B 91 THR cc_start: 0.8732 (m) cc_final: 0.8226 (p) REVERT: B 99 VAL cc_start: 0.9071 (t) cc_final: 0.8725 (t) REVERT: B 101 PHE cc_start: 0.8635 (m-80) cc_final: 0.8397 (m-10) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.1557 time to fit residues: 23.8803 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 : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 overall best weight: 0.4934 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3373 Z= 0.217 Angle : 0.725 7.009 4593 Z= 0.378 Chirality : 0.047 0.180 512 Planarity : 0.007 0.105 588 Dihedral : 6.785 31.246 498 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.49 % Favored : 89.27 % 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: -2.54 (0.39), residues: 410 helix: -4.78 (0.67), residues: 14 sheet: -1.14 (0.43), residues: 132 loop : -1.87 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 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 408 *********************** 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 : 0.373 Fit side-chains revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7764 (m-80) cc_final: 0.7500 (m-80) REVERT: R 428 ASP cc_start: 0.8020 (t0) cc_final: 0.7377 (t0) REVERT: R 474 GLN cc_start: 0.6038 (OUTLIER) cc_final: 0.5495 (tm-30) REVERT: R 496 SER cc_start: 0.8420 (t) cc_final: 0.7903 (p) REVERT: A 4 LEU cc_start: 0.9139 (mm) cc_final: 0.8868 (mm) REVERT: A 41 GLN cc_start: 0.8815 (tp40) cc_final: 0.8515 (tp40) REVERT: A 61 TYR cc_start: 0.6256 (m-80) cc_final: 0.5699 (m-80) REVERT: A 62 ASN cc_start: 0.9048 (t0) cc_final: 0.8554 (t0) REVERT: A 111 ASP cc_start: 0.9084 (t0) cc_final: 0.8672 (t0) REVERT: A 115 MET cc_start: 0.8350 (tpt) cc_final: 0.8054 (tpp) REVERT: A 121 MET cc_start: 0.7067 (ptt) cc_final: 0.6626 (ppp) REVERT: B 36 TRP cc_start: 0.8311 (m100) cc_final: 0.8081 (m100) REVERT: B 91 THR cc_start: 0.8417 (m) cc_final: 0.8133 (m) REVERT: B 106 ARG cc_start: 0.8868 (mtm110) cc_final: 0.8619 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1470 time to fit residues: 21.3921 Evaluate side-chains 93 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3373 Z= 0.198 Angle : 0.723 9.219 4593 Z= 0.362 Chirality : 0.047 0.200 512 Planarity : 0.007 0.109 588 Dihedral : 6.571 31.199 498 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.51 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -2.27 (0.41), residues: 410 helix: -4.84 (0.63), residues: 14 sheet: -1.02 (0.44), residues: 131 loop : -1.62 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 49 HIS 0.005 0.001 HIS A 99 PHE 0.025 0.002 PHE R 464 TYR 0.016 0.001 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 124 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 365 TYR cc_start: 0.7822 (m-80) cc_final: 0.7372 (m-80) REVERT: R 428 ASP cc_start: 0.8052 (t0) cc_final: 0.7433 (t0) REVERT: A 40 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7250 (ttm-80) REVERT: A 61 TYR cc_start: 0.6580 (m-80) cc_final: 0.5753 (m-80) REVERT: A 62 ASN cc_start: 0.9004 (t0) cc_final: 0.8654 (t0) REVERT: A 115 MET cc_start: 0.8335 (tpt) cc_final: 0.8013 (tpp) REVERT: A 121 MET cc_start: 0.7250 (ptt) cc_final: 0.6677 (ppp) REVERT: B 36 TRP cc_start: 0.8525 (m100) cc_final: 0.8103 (m100) REVERT: B 49 ILE cc_start: 0.8188 (tp) cc_final: 0.7961 (tp) REVERT: B 90 GLU cc_start: 0.7770 (pt0) cc_final: 0.7439 (pt0) REVERT: B 99 VAL cc_start: 0.9080 (t) cc_final: 0.8531 (t) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1560 time to fit residues: 23.5316 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 28 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3373 Z= 0.225 Angle : 0.705 6.241 4593 Z= 0.362 Chirality : 0.046 0.180 512 Planarity : 0.006 0.091 588 Dihedral : 6.504 31.690 498 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.51 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % 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: -2.09 (0.41), residues: 410 helix: -4.78 (0.68), residues: 14 sheet: -0.91 (0.45), residues: 126 loop : -1.48 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 49 HIS 0.005 0.002 HIS A 99 PHE 0.016 0.002 PHE R 456 TYR 0.013 0.002 TYR R 423 ARG 0.006 0.001 ARG R 408 *********************** 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 120 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: R 402 ILE cc_start: 0.8802 (tt) cc_final: 0.8533 (tt) REVERT: R 428 ASP cc_start: 0.8196 (t0) cc_final: 0.7550 (t0) REVERT: R 465 GLU cc_start: 0.7370 (pp20) cc_final: 0.7166 (tm-30) REVERT: A 4 LEU cc_start: 0.9292 (mm) cc_final: 0.9082 (mm) REVERT: A 13 LYS cc_start: 0.3949 (mmtt) cc_final: 0.3179 (mmmt) REVERT: A 61 TYR cc_start: 0.6721 (m-80) cc_final: 0.6315 (m-80) REVERT: A 115 MET cc_start: 0.8382 (tpt) cc_final: 0.8174 (tpp) REVERT: A 121 MET cc_start: 0.7427 (ptt) cc_final: 0.6705 (ppp) REVERT: B 36 TRP cc_start: 0.8579 (m100) cc_final: 0.8220 (m100) REVERT: B 37 TYR cc_start: 0.7601 (m-10) cc_final: 0.6305 (m-10) REVERT: B 49 ILE cc_start: 0.8440 (tp) cc_final: 0.8198 (tp) REVERT: B 89 CYS cc_start: 0.6156 (p) cc_final: 0.5715 (p) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1454 time to fit residues: 21.3217 Evaluate side-chains 88 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5590 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= 0.311 Angle : 0.765 9.109 4593 Z= 0.395 Chirality : 0.048 0.147 512 Planarity : 0.007 0.118 588 Dihedral : 6.852 34.552 498 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -2.12 (0.42), residues: 410 helix: -4.01 (0.75), residues: 20 sheet: -0.94 (0.45), residues: 135 loop : -1.47 (0.41), residues: 255 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 0.020 0.002 PHE R 377 TYR 0.019 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 123 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 365 TYR cc_start: 0.8106 (m-80) cc_final: 0.7643 (m-80) REVERT: R 386 LYS cc_start: 0.8274 (pttt) cc_final: 0.7895 (pttp) REVERT: R 428 ASP cc_start: 0.8298 (t0) cc_final: 0.7811 (t70) REVERT: R 500 THR cc_start: 0.8977 (p) cc_final: 0.8486 (t) REVERT: A 4 LEU cc_start: 0.9302 (mm) cc_final: 0.9044 (mm) REVERT: A 61 TYR cc_start: 0.6717 (m-80) cc_final: 0.6202 (m-80) REVERT: A 62 ASN cc_start: 0.8871 (t0) cc_final: 0.8286 (t0) REVERT: A 97 CYS cc_start: 0.5083 (p) cc_final: 0.4663 (p) REVERT: A 121 MET cc_start: 0.7645 (ptt) cc_final: 0.6874 (ppp) REVERT: B 36 TRP cc_start: 0.8580 (m100) cc_final: 0.8212 (m100) REVERT: B 49 ILE cc_start: 0.8704 (tp) cc_final: 0.8474 (tp) REVERT: B 52 ASN cc_start: 0.6493 (m-40) cc_final: 0.6268 (m-40) REVERT: B 89 CYS cc_start: 0.6074 (p) cc_final: 0.5191 (p) REVERT: B 93 ASP cc_start: 0.7646 (t0) cc_final: 0.7349 (t0) REVERT: B 99 VAL cc_start: 0.9082 (t) cc_final: 0.8727 (t) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1392 time to fit residues: 20.8888 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 : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3373 Z= 0.239 Angle : 0.740 6.761 4593 Z= 0.382 Chirality : 0.047 0.182 512 Planarity : 0.007 0.100 588 Dihedral : 6.747 35.357 498 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.51 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -2.12 (0.41), residues: 410 helix: -3.78 (0.86), residues: 20 sheet: -0.93 (0.45), residues: 135 loop : -1.49 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 49 HIS 0.005 0.002 HIS A 99 PHE 0.022 0.002 PHE R 377 TYR 0.021 0.002 TYR B 50 ARG 0.004 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 : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 386 LYS cc_start: 0.8282 (pttt) cc_final: 0.7950 (pttp) REVERT: R 428 ASP cc_start: 0.8334 (t0) cc_final: 0.7829 (t70) REVERT: R 500 THR cc_start: 0.8917 (p) cc_final: 0.8389 (t) REVERT: A 4 LEU cc_start: 0.9262 (mm) cc_final: 0.9049 (mm) REVERT: A 13 LYS cc_start: 0.4126 (mmtt) cc_final: 0.3330 (mmmt) REVERT: A 49 TRP cc_start: 0.8202 (t60) cc_final: 0.7888 (t60) REVERT: A 66 LYS cc_start: 0.8945 (mmpt) cc_final: 0.8726 (mmmt) REVERT: A 97 CYS cc_start: 0.5020 (p) cc_final: 0.4775 (p) REVERT: A 121 MET cc_start: 0.7653 (ptt) cc_final: 0.6921 (ppp) REVERT: B 36 TRP cc_start: 0.8611 (m100) cc_final: 0.8283 (m100) REVERT: B 37 TYR cc_start: 0.7805 (m-10) cc_final: 0.6688 (m-10) REVERT: B 89 CYS cc_start: 0.6091 (p) cc_final: 0.5442 (p) REVERT: B 90 GLU cc_start: 0.7705 (pt0) cc_final: 0.7016 (pt0) REVERT: B 93 ASP cc_start: 0.7579 (t0) cc_final: 0.7219 (t0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1469 time to fit residues: 21.9698 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 : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3373 Z= 0.222 Angle : 0.724 6.424 4593 Z= 0.372 Chirality : 0.047 0.182 512 Planarity : 0.006 0.091 588 Dihedral : 6.729 36.247 498 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -2.17 (0.41), residues: 410 helix: -3.72 (0.88), residues: 20 sheet: -0.90 (0.46), residues: 135 loop : -1.59 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 436 HIS 0.004 0.002 HIS A 99 PHE 0.016 0.002 PHE R 377 TYR 0.010 0.001 TYR R 495 ARG 0.005 0.001 ARG B 31 *********************** 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 129 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: R 386 LYS cc_start: 0.8335 (pttt) cc_final: 0.8069 (pttp) REVERT: R 428 ASP cc_start: 0.8395 (t0) cc_final: 0.7887 (t70) REVERT: R 500 THR cc_start: 0.8912 (p) cc_final: 0.8408 (t) REVERT: A 13 LYS cc_start: 0.4340 (mmtt) cc_final: 0.3554 (mmmt) REVERT: A 40 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.7890 (ttm-80) REVERT: A 61 TYR cc_start: 0.7152 (m-80) cc_final: 0.6931 (m-80) REVERT: A 97 CYS cc_start: 0.4977 (p) cc_final: 0.4635 (p) REVERT: A 121 MET cc_start: 0.7690 (ptt) cc_final: 0.7107 (ppp) REVERT: B 37 TYR cc_start: 0.7767 (m-10) cc_final: 0.6662 (m-10) REVERT: B 89 CYS cc_start: 0.6075 (p) cc_final: 0.5132 (p) REVERT: B 90 GLU cc_start: 0.7701 (pt0) cc_final: 0.7045 (pt0) REVERT: B 93 ASP cc_start: 0.7382 (t0) cc_final: 0.7112 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1491 time to fit residues: 23.5353 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3373 Z= 0.232 Angle : 0.780 11.692 4593 Z= 0.394 Chirality : 0.048 0.203 512 Planarity : 0.006 0.087 588 Dihedral : 6.743 36.573 498 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.27 % Favored : 90.49 % 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: -2.17 (0.41), residues: 410 helix: -3.90 (0.79), residues: 20 sheet: -0.80 (0.46), residues: 133 loop : -1.63 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 36 HIS 0.004 0.002 HIS A 99 PHE 0.016 0.002 PHE R 377 TYR 0.026 0.002 TYR B 50 ARG 0.004 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 134 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: R 405 ASP cc_start: 0.8852 (t0) cc_final: 0.8526 (t0) REVERT: R 428 ASP cc_start: 0.8340 (t0) cc_final: 0.7846 (t70) REVERT: R 500 THR cc_start: 0.8917 (p) cc_final: 0.8442 (t) REVERT: A 13 LYS cc_start: 0.4820 (mmtt) cc_final: 0.4107 (mmmt) REVERT: A 15 LYS cc_start: 0.8692 (tppt) cc_final: 0.7964 (tmmt) REVERT: A 40 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.7790 (ttm-80) REVERT: A 49 TRP cc_start: 0.8358 (t60) cc_final: 0.7652 (t60) REVERT: A 61 TYR cc_start: 0.7116 (m-80) cc_final: 0.6544 (m-80) REVERT: A 62 ASN cc_start: 0.8962 (t0) cc_final: 0.8245 (t0) REVERT: A 97 CYS cc_start: 0.4727 (p) cc_final: 0.4485 (p) REVERT: A 121 MET cc_start: 0.7575 (ptt) cc_final: 0.7030 (ppp) REVERT: B 52 ASN cc_start: 0.6879 (m-40) cc_final: 0.5706 (m-40) REVERT: B 90 GLU cc_start: 0.7710 (pt0) cc_final: 0.6715 (pt0) REVERT: B 99 VAL cc_start: 0.9097 (t) cc_final: 0.8782 (t) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1352 time to fit residues: 22.3593 Evaluate side-chains 101 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0040 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6476 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 : 0.777 9.382 4593 Z= 0.394 Chirality : 0.048 0.179 512 Planarity : 0.006 0.085 588 Dihedral : 6.973 39.328 498 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.73 % 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 : 0.51 % 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: -2.17 (0.41), residues: 410 helix: -3.56 (0.87), residues: 20 sheet: -0.83 (0.46), residues: 135 loop : -1.64 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 36 HIS 0.004 0.002 HIS B 51 PHE 0.016 0.002 PHE R 377 TYR 0.014 0.001 TYR B 37 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 129 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 405 ASP cc_start: 0.8869 (t0) cc_final: 0.8490 (t0) REVERT: R 428 ASP cc_start: 0.8342 (t0) cc_final: 0.7834 (t70) REVERT: R 500 THR cc_start: 0.8902 (p) cc_final: 0.8366 (t) REVERT: A 13 LYS cc_start: 0.5003 (mmtt) cc_final: 0.4295 (mmmt) REVERT: A 15 LYS cc_start: 0.8709 (tppt) cc_final: 0.7960 (tmmt) REVERT: A 49 TRP cc_start: 0.8153 (t60) cc_final: 0.7490 (t60) REVERT: A 61 TYR cc_start: 0.7134 (m-80) cc_final: 0.6372 (m-80) REVERT: A 62 ASN cc_start: 0.8970 (t0) cc_final: 0.8091 (t0) REVERT: A 96 PHE cc_start: 0.9305 (m-80) cc_final: 0.8774 (m-80) REVERT: A 97 CYS cc_start: 0.4817 (p) cc_final: 0.4554 (p) REVERT: A 121 MET cc_start: 0.7634 (ptt) cc_final: 0.7005 (ppp) REVERT: B 36 TRP cc_start: 0.8518 (m100) cc_final: 0.8198 (m100) REVERT: B 52 ASN cc_start: 0.6982 (m-40) cc_final: 0.5959 (m-40) REVERT: B 89 CYS cc_start: 0.5857 (p) cc_final: 0.5141 (p) REVERT: B 90 GLU cc_start: 0.7831 (pt0) cc_final: 0.7233 (pt0) REVERT: B 93 ASP cc_start: 0.7546 (t0) cc_final: 0.7104 (t0) REVERT: B 99 VAL cc_start: 0.9088 (t) cc_final: 0.8800 (t) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1336 time to fit residues: 21.3864 Evaluate side-chains 104 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.1980 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.0030 chunk 14 optimal weight: 0.0070 chunk 39 optimal weight: 2.9990 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 409 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3897 r_free = 0.3897 target = 0.135053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117059 restraints weight = 8505.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.120462 restraints weight = 5132.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.122826 restraints weight = 3519.347| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3373 Z= 0.194 Angle : 0.747 8.582 4593 Z= 0.374 Chirality : 0.047 0.182 512 Planarity : 0.006 0.083 588 Dihedral : 6.688 37.295 498 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.51 % Favored : 90.24 % 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: -2.17 (0.41), residues: 410 helix: -3.87 (0.72), residues: 26 sheet: -0.67 (0.47), residues: 131 loop : -1.64 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 36 HIS 0.004 0.002 HIS A 99 PHE 0.016 0.001 PHE R 377 TYR 0.009 0.001 TYR B 87 ARG 0.004 0.001 ARG R 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.34 seconds wall clock time: 28 minutes 20.41 seconds (1700.41 seconds total)