Starting phenix.real_space_refine on Fri Dec 27 23:50:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvh_42620/12_2024/8uvh_42620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvh_42620/12_2024/8uvh_42620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvh_42620/12_2024/8uvh_42620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvh_42620/12_2024/8uvh_42620.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvh_42620/12_2024/8uvh_42620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvh_42620/12_2024/8uvh_42620.cif" } resolution = 2.33 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= 0.003 sd= 0.066 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 60 5.16 5 C 4786 2.51 5 N 1126 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7158 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3579 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 29, 'TRANS': 429} Chain breaks: 5 Restraints were copied for chains: B Time building chain proxies: 6.28, per 1000 atoms: 0.88 Number of scatterers: 7158 At special positions: 0 Unit cell: (76.725, 99.825, 79.2, 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 60 16.00 O 1186 8.00 N 1126 7.00 C 4786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.610A pdb=" N LEU A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 removed outlier: 4.421A pdb=" N LEU A 25 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 52 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.515A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 84 through 103 Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.588A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 140 through 158 Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.520A pdb=" N ILE A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.593A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 276 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 292 through 308 Processing helix chain 'A' and resid 313 through 334 removed outlier: 4.135A pdb=" N ASP A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 398 through 406 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 444 through 460 Processing helix chain 'A' and resid 464 through 483 Proline residue: A 474 - end of helix Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.654A pdb=" N ILE A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 508 through 517 removed outlier: 4.026A pdb=" N TYR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.878A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 558 through 562 Processing helix chain 'B' and resid 14 through 20 Processing helix chain 'B' and resid 21 through 25 removed outlier: 4.421A pdb=" N LEU B 25 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 52 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.515A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 84 through 103 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.588A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 Processing helix chain 'B' and resid 140 through 158 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 202 through 220 removed outlier: 3.520A pdb=" N ILE B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.592A pdb=" N VAL B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 276 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 292 through 308 Processing helix chain 'B' and resid 313 through 334 removed outlier: 4.135A pdb=" N ASP B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 368 Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 428 through 437 Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 464 through 483 Proline residue: B 474 - end of helix Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.654A pdb=" N ILE B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 508 through 517 removed outlier: 4.025A pdb=" N TYR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 547 removed outlier: 3.878A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 558 through 562 512 hydrogen bonds defined for protein. 1512 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: 2.21 Time building geometry restraints manager: 2.11 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: 1131 1.33 - 1.45: 1881 1.45 - 1.57: 4234 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 7346 Sorted by residual: bond pdb=" C PRO B 444 " pdb=" O PRO B 444 " ideal model delta sigma weight residual 1.240 1.205 0.035 1.12e-02 7.97e+03 9.79e+00 bond pdb=" C PRO A 444 " pdb=" O PRO A 444 " ideal model delta sigma weight residual 1.240 1.206 0.035 1.12e-02 7.97e+03 9.54e+00 bond pdb=" CA SER B 60 " pdb=" CB SER B 60 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.74e-02 3.30e+03 6.30e+00 bond pdb=" N LEU B 440 " pdb=" CA LEU B 440 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.26e+00 bond pdb=" CA SER A 60 " pdb=" CB SER A 60 " ideal model delta sigma weight residual 1.529 1.486 0.043 1.74e-02 3.30e+03 6.21e+00 ... (remaining 7341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 9657 1.41 - 2.82: 260 2.82 - 4.23: 69 4.23 - 5.64: 28 5.64 - 7.05: 4 Bond angle restraints: 10018 Sorted by residual: angle pdb=" N HIS A 441 " pdb=" CA HIS A 441 " pdb=" C HIS A 441 " ideal model delta sigma weight residual 113.20 107.59 5.61 1.21e+00 6.83e-01 2.15e+01 angle pdb=" N HIS B 441 " pdb=" CA HIS B 441 " pdb=" C HIS B 441 " ideal model delta sigma weight residual 113.20 107.60 5.60 1.21e+00 6.83e-01 2.15e+01 angle pdb=" N LEU A 440 " pdb=" CA LEU A 440 " pdb=" C LEU A 440 " ideal model delta sigma weight residual 113.02 107.80 5.22 1.20e+00 6.94e-01 1.89e+01 angle pdb=" N LEU B 440 " pdb=" CA LEU B 440 " pdb=" C LEU B 440 " ideal model delta sigma weight residual 113.02 107.80 5.22 1.20e+00 6.94e-01 1.89e+01 angle pdb=" CA PRO A 444 " pdb=" C PRO A 444 " pdb=" N PRO A 445 " ideal model delta sigma weight residual 117.93 122.31 -4.38 1.20e+00 6.94e-01 1.33e+01 ... (remaining 10013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 4018 16.77 - 33.55: 258 33.55 - 50.32: 34 50.32 - 67.10: 10 67.10 - 83.87: 6 Dihedral angle restraints: 4326 sinusoidal: 1656 harmonic: 2670 Sorted by residual: dihedral pdb=" CA PHE A 18 " pdb=" C PHE A 18 " pdb=" N VAL A 19 " pdb=" CA VAL A 19 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PHE B 18 " pdb=" C PHE B 18 " pdb=" N VAL B 19 " pdb=" CA VAL B 19 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU B 65 " pdb=" C LEU B 65 " pdb=" N LEU B 66 " pdb=" CA LEU B 66 " ideal model delta harmonic sigma weight residual -180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 4323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 973 0.050 - 0.101: 200 0.101 - 0.151: 35 0.151 - 0.201: 0 0.201 - 0.251: 4 Chirality restraints: 1212 Sorted by residual: chirality pdb=" CA TYR A 82 " pdb=" N TYR A 82 " pdb=" C TYR A 82 " pdb=" CB TYR A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA TYR B 82 " pdb=" N TYR B 82 " pdb=" C TYR B 82 " pdb=" CB TYR B 82 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA LEU A 440 " pdb=" N LEU A 440 " pdb=" C LEU A 440 " pdb=" CB LEU A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1209 not shown) Planarity restraints: 1200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 437 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C MET A 437 " -0.060 2.00e-02 2.50e+03 pdb=" O MET A 437 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 438 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 437 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C MET B 437 " 0.060 2.00e-02 2.50e+03 pdb=" O MET B 437 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU B 438 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 82 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C TYR B 82 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR B 82 " 0.019 2.00e-02 2.50e+03 pdb=" N MET B 83 " 0.018 2.00e-02 2.50e+03 ... (remaining 1197 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1625 2.78 - 3.31: 7503 3.31 - 3.84: 12860 3.84 - 4.37: 15004 4.37 - 4.90: 25992 Nonbonded interactions: 62984 Sorted by model distance: nonbonded pdb=" O MET B 137 " pdb=" OG1 THR B 223 " model vdw 2.255 3.040 nonbonded pdb=" O MET A 137 " pdb=" OG1 THR A 223 " model vdw 2.256 3.040 nonbonded pdb=" O SER B 60 " pdb=" OH TYR B 82 " model vdw 2.281 3.040 nonbonded pdb=" O SER A 60 " pdb=" OH TYR A 82 " model vdw 2.282 3.040 nonbonded pdb=" O SER B 464 " pdb=" OG1 THR B 468 " model vdw 2.284 3.040 ... (remaining 62979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.990 Find NCS groups from input model: 0.180 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:15.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.004 0.044 7346 Z= 0.222 Angle : 0.640 7.046 10018 Z= 0.365 Chirality : 0.043 0.251 1212 Planarity : 0.006 0.048 1200 Dihedral : 11.896 83.869 2582 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % 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: 2.35 (0.28), residues: 894 helix: 2.04 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -0.20 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 49 HIS 0.003 0.001 HIS A 106 PHE 0.010 0.001 PHE A 18 TYR 0.025 0.002 TYR B 214 ARG 0.003 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.825 Fit side-chains REVERT: A 16 ILE cc_start: 0.7210 (tp) cc_final: 0.6979 (pp) REVERT: A 123 ARG cc_start: 0.5443 (ptp-110) cc_final: 0.5044 (ttm110) REVERT: A 455 LEU cc_start: 0.6828 (mt) cc_final: 0.6215 (tp) REVERT: A 532 MET cc_start: 0.7610 (mmt) cc_final: 0.7172 (mmm) REVERT: B 16 ILE cc_start: 0.7225 (tp) cc_final: 0.7011 (pp) REVERT: B 123 ARG cc_start: 0.5376 (ptp-110) cc_final: 0.4870 (ptp-170) REVERT: B 125 MET cc_start: 0.8134 (ttm) cc_final: 0.7923 (ttp) REVERT: B 261 MET cc_start: 0.7772 (tmm) cc_final: 0.7538 (tmm) REVERT: B 455 LEU cc_start: 0.7003 (mt) cc_final: 0.6473 (tp) REVERT: B 491 MET cc_start: 0.7493 (mtp) cc_final: 0.6995 (mtp) REVERT: B 534 ILE cc_start: 0.7404 (mt) cc_final: 0.7118 (tp) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 1.0661 time to fit residues: 165.5223 Evaluate side-chains 120 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain B residue 60 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 81 optimal weight: 0.0970 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7346 Z= 0.219 Angle : 0.575 5.937 10018 Z= 0.297 Chirality : 0.042 0.162 1212 Planarity : 0.006 0.051 1200 Dihedral : 4.343 20.980 952 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.89 % Allowed : 5.36 % Favored : 93.75 % 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: 2.62 (0.28), residues: 894 helix: 2.19 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.14 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 399 HIS 0.006 0.002 HIS B 441 PHE 0.014 0.001 PHE A 35 TYR 0.007 0.001 TYR B 82 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 16 ILE cc_start: 0.7496 (tp) cc_final: 0.7232 (pt) REVERT: A 123 ARG cc_start: 0.5274 (ptp-110) cc_final: 0.4741 (ptp-170) REVERT: A 267 PHE cc_start: 0.7895 (m-80) cc_final: 0.7650 (m-10) REVERT: A 455 LEU cc_start: 0.6956 (mt) cc_final: 0.6283 (tp) REVERT: A 545 ASN cc_start: 0.7970 (m-40) cc_final: 0.7707 (m110) REVERT: B 123 ARG cc_start: 0.5307 (ptp-110) cc_final: 0.4836 (ptp-170) REVERT: B 208 MET cc_start: 0.7724 (mmm) cc_final: 0.7378 (mmp) REVERT: B 261 MET cc_start: 0.7851 (tmm) cc_final: 0.7650 (tmm) REVERT: B 455 LEU cc_start: 0.6849 (mt) cc_final: 0.6306 (tp) REVERT: B 491 MET cc_start: 0.7578 (mtp) cc_final: 0.7047 (mtp) REVERT: B 534 ILE cc_start: 0.7382 (mt) cc_final: 0.7143 (tp) outliers start: 7 outliers final: 3 residues processed: 134 average time/residue: 1.1714 time to fit residues: 167.2765 Evaluate side-chains 122 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 77 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7346 Z= 0.180 Angle : 0.544 5.671 10018 Z= 0.279 Chirality : 0.041 0.135 1212 Planarity : 0.006 0.052 1200 Dihedral : 4.249 21.768 950 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.02 % Allowed : 7.65 % Favored : 91.33 % 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: 2.71 (0.28), residues: 894 helix: 2.24 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.05 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 399 HIS 0.003 0.001 HIS A 106 PHE 0.012 0.001 PHE A 35 TYR 0.007 0.001 TYR B 48 ARG 0.002 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.804 Fit side-chains REVERT: A 16 ILE cc_start: 0.7516 (tp) cc_final: 0.7233 (pt) REVERT: A 123 ARG cc_start: 0.5247 (ptp-110) cc_final: 0.4722 (ptp-170) REVERT: A 267 PHE cc_start: 0.7906 (m-80) cc_final: 0.7650 (m-10) REVERT: A 425 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7119 (mp0) REVERT: A 455 LEU cc_start: 0.6964 (mt) cc_final: 0.6310 (tp) REVERT: A 553 ASP cc_start: 0.7274 (t0) cc_final: 0.6754 (t70) REVERT: B 123 ARG cc_start: 0.5284 (ptp-110) cc_final: 0.4845 (ptp-170) REVERT: B 261 MET cc_start: 0.7840 (tmm) cc_final: 0.7602 (tmm) REVERT: B 425 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: B 455 LEU cc_start: 0.6804 (mt) cc_final: 0.6346 (tp) REVERT: B 491 MET cc_start: 0.7553 (mtp) cc_final: 0.7018 (mtp) outliers start: 8 outliers final: 5 residues processed: 128 average time/residue: 1.1251 time to fit residues: 154.0348 Evaluate side-chains 123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 425 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 77 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7346 Z= 0.202 Angle : 0.556 6.039 10018 Z= 0.285 Chirality : 0.041 0.135 1212 Planarity : 0.006 0.053 1200 Dihedral : 4.270 27.056 950 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.28 % Allowed : 8.55 % Favored : 90.18 % 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: 2.69 (0.28), residues: 894 helix: 2.22 (0.20), residues: 718 sheet: None (None), residues: 0 loop : 0.02 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 399 HIS 0.005 0.001 HIS A 106 PHE 0.014 0.001 PHE A 35 TYR 0.009 0.001 TYR B 48 ARG 0.002 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.933 Fit side-chains REVERT: A 16 ILE cc_start: 0.7522 (tp) cc_final: 0.7236 (pt) REVERT: A 123 ARG cc_start: 0.5251 (ptp-110) cc_final: 0.4955 (ttm110) REVERT: A 267 PHE cc_start: 0.7905 (m-80) cc_final: 0.7655 (m-10) REVERT: A 425 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7027 (mp0) REVERT: A 455 LEU cc_start: 0.6977 (mt) cc_final: 0.6309 (tp) REVERT: A 459 PHE cc_start: 0.6349 (t80) cc_final: 0.5773 (t80) REVERT: A 553 ASP cc_start: 0.7304 (t0) cc_final: 0.6805 (t70) REVERT: B 261 MET cc_start: 0.7858 (tmm) cc_final: 0.7615 (tmm) REVERT: B 425 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: B 455 LEU cc_start: 0.6840 (mt) cc_final: 0.6363 (tp) REVERT: B 491 MET cc_start: 0.7558 (mtp) cc_final: 0.7109 (mtp) outliers start: 10 outliers final: 6 residues processed: 127 average time/residue: 1.0478 time to fit residues: 141.8506 Evaluate side-chains 123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 425 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.0040 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 71 GLN B 77 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7346 Z= 0.224 Angle : 0.577 6.088 10018 Z= 0.295 Chirality : 0.042 0.133 1212 Planarity : 0.006 0.055 1200 Dihedral : 4.345 31.845 950 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.15 % Allowed : 9.57 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 2.54 (0.29), residues: 894 helix: 2.09 (0.20), residues: 724 sheet: None (None), residues: 0 loop : 0.01 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 399 HIS 0.006 0.001 HIS B 106 PHE 0.015 0.001 PHE A 35 TYR 0.016 0.001 TYR B 489 ARG 0.004 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.726 Fit side-chains REVERT: A 123 ARG cc_start: 0.5295 (ptp-110) cc_final: 0.4993 (ttm110) REVERT: A 373 GLN cc_start: 0.7720 (mt0) cc_final: 0.7422 (mt0) REVERT: A 455 LEU cc_start: 0.6940 (mt) cc_final: 0.6283 (tp) REVERT: A 459 PHE cc_start: 0.6355 (t80) cc_final: 0.5751 (t80) REVERT: A 553 ASP cc_start: 0.7360 (t0) cc_final: 0.6881 (t70) REVERT: B 52 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6665 (mt-10) REVERT: B 123 ARG cc_start: 0.5539 (ptp-110) cc_final: 0.4625 (ptp-170) REVERT: B 261 MET cc_start: 0.7885 (tmm) cc_final: 0.7548 (tmm) REVERT: B 425 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: B 455 LEU cc_start: 0.6809 (mt) cc_final: 0.6343 (tp) REVERT: B 491 MET cc_start: 0.7591 (mtp) cc_final: 0.7073 (mtp) outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 1.0452 time to fit residues: 137.3720 Evaluate side-chains 118 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 425 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 77 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7346 Z= 0.175 Angle : 0.536 5.738 10018 Z= 0.275 Chirality : 0.040 0.143 1212 Planarity : 0.006 0.054 1200 Dihedral : 4.225 29.328 950 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.28 % Allowed : 9.95 % Favored : 88.78 % 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: 2.66 (0.29), residues: 894 helix: 2.17 (0.20), residues: 724 sheet: None (None), residues: 0 loop : 0.05 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 399 HIS 0.004 0.001 HIS B 106 PHE 0.010 0.001 PHE A 35 TYR 0.009 0.001 TYR A 48 ARG 0.002 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.932 Fit side-chains REVERT: A 123 ARG cc_start: 0.5293 (ptp-110) cc_final: 0.5000 (ttm110) REVERT: A 373 GLN cc_start: 0.7729 (mt0) cc_final: 0.7431 (mt0) REVERT: A 455 LEU cc_start: 0.6985 (mt) cc_final: 0.6352 (tp) REVERT: A 459 PHE cc_start: 0.6391 (t80) cc_final: 0.5778 (t80) REVERT: A 553 ASP cc_start: 0.7336 (t0) cc_final: 0.6880 (t70) REVERT: B 52 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6603 (mt-10) REVERT: B 123 ARG cc_start: 0.5437 (ptp-110) cc_final: 0.4602 (ptp-170) REVERT: B 261 MET cc_start: 0.7864 (tmm) cc_final: 0.7620 (tmm) REVERT: B 425 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: B 455 LEU cc_start: 0.6774 (mt) cc_final: 0.6334 (tp) REVERT: B 491 MET cc_start: 0.7526 (mtp) cc_final: 0.7005 (mtp) outliers start: 10 outliers final: 3 residues processed: 126 average time/residue: 1.0110 time to fit residues: 136.1772 Evaluate side-chains 119 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 425 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 77 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7346 Z= 0.192 Angle : 0.546 5.847 10018 Z= 0.279 Chirality : 0.041 0.145 1212 Planarity : 0.005 0.054 1200 Dihedral : 4.238 28.665 950 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.77 % Allowed : 11.10 % Favored : 88.14 % 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: 2.65 (0.29), residues: 894 helix: 2.16 (0.19), residues: 724 sheet: None (None), residues: 0 loop : 0.03 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 399 HIS 0.005 0.001 HIS A 106 PHE 0.012 0.001 PHE A 35 TYR 0.020 0.001 TYR B 489 ARG 0.002 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.822 Fit side-chains REVERT: A 123 ARG cc_start: 0.5327 (ptp-110) cc_final: 0.5037 (ttm110) REVERT: A 373 GLN cc_start: 0.7741 (mt0) cc_final: 0.7443 (mt0) REVERT: A 425 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7163 (tm-30) REVERT: A 455 LEU cc_start: 0.6984 (mt) cc_final: 0.6357 (tp) REVERT: A 459 PHE cc_start: 0.6440 (t80) cc_final: 0.5821 (t80) REVERT: A 553 ASP cc_start: 0.7352 (t0) cc_final: 0.6906 (t70) REVERT: B 52 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6618 (mt-10) REVERT: B 123 ARG cc_start: 0.5432 (ptp-110) cc_final: 0.4616 (ptp-170) REVERT: B 261 MET cc_start: 0.7823 (tmm) cc_final: 0.7597 (tmm) REVERT: B 425 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: B 455 LEU cc_start: 0.6779 (mt) cc_final: 0.6330 (tp) REVERT: B 491 MET cc_start: 0.7547 (mtp) cc_final: 0.7029 (mtp) outliers start: 6 outliers final: 3 residues processed: 120 average time/residue: 1.0496 time to fit residues: 134.2783 Evaluate side-chains 116 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 425 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 71 GLN B 77 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7346 Z= 0.287 Angle : 0.632 6.909 10018 Z= 0.319 Chirality : 0.044 0.143 1212 Planarity : 0.006 0.056 1200 Dihedral : 4.436 28.171 950 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.15 % Allowed : 10.84 % Favored : 88.01 % 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: 2.39 (0.28), residues: 894 helix: 1.96 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.04 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 399 HIS 0.007 0.001 HIS A 106 PHE 0.019 0.002 PHE A 35 TYR 0.010 0.001 TYR B 214 ARG 0.003 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.805 Fit side-chains REVERT: A 373 GLN cc_start: 0.7749 (mt0) cc_final: 0.7460 (mt0) REVERT: A 425 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7124 (tm-30) REVERT: A 455 LEU cc_start: 0.6976 (mt) cc_final: 0.6382 (tp) REVERT: A 459 PHE cc_start: 0.6501 (t80) cc_final: 0.5861 (t80) REVERT: A 553 ASP cc_start: 0.7472 (t0) cc_final: 0.6999 (t70) REVERT: B 123 ARG cc_start: 0.5487 (ptp-110) cc_final: 0.4659 (ptp-170) REVERT: B 261 MET cc_start: 0.7910 (tmm) cc_final: 0.7599 (tmm) REVERT: B 425 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: B 455 LEU cc_start: 0.6835 (mt) cc_final: 0.6392 (tp) REVERT: B 491 MET cc_start: 0.7675 (mtp) cc_final: 0.7240 (mtp) outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 1.0732 time to fit residues: 136.3562 Evaluate side-chains 121 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 425 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 77 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7346 Z= 0.217 Angle : 0.587 6.405 10018 Z= 0.297 Chirality : 0.042 0.141 1212 Planarity : 0.006 0.056 1200 Dihedral : 4.368 27.666 950 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.02 % Allowed : 11.61 % Favored : 87.37 % 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: 2.48 (0.28), residues: 894 helix: 2.00 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.16 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 399 HIS 0.006 0.001 HIS A 106 PHE 0.013 0.001 PHE A 35 TYR 0.010 0.001 TYR B 214 ARG 0.003 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.961 Fit side-chains REVERT: A 308 LYS cc_start: 0.7901 (mttm) cc_final: 0.7651 (mttt) REVERT: A 373 GLN cc_start: 0.7744 (mt0) cc_final: 0.7456 (mt0) REVERT: A 425 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7116 (tm-30) REVERT: A 455 LEU cc_start: 0.6960 (mt) cc_final: 0.6378 (tp) REVERT: A 459 PHE cc_start: 0.6503 (t80) cc_final: 0.5867 (t80) REVERT: A 553 ASP cc_start: 0.7447 (t0) cc_final: 0.6973 (t70) REVERT: B 123 ARG cc_start: 0.5465 (ptp-110) cc_final: 0.4637 (ptp-170) REVERT: B 425 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: B 455 LEU cc_start: 0.6824 (mt) cc_final: 0.6391 (tp) REVERT: B 491 MET cc_start: 0.7589 (mtp) cc_final: 0.7067 (mtp) outliers start: 8 outliers final: 5 residues processed: 119 average time/residue: 1.1034 time to fit residues: 140.1385 Evaluate side-chains 123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 425 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.0970 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 76 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 77 GLN B 465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7346 Z= 0.178 Angle : 0.563 5.910 10018 Z= 0.285 Chirality : 0.040 0.144 1212 Planarity : 0.005 0.055 1200 Dihedral : 4.289 27.350 950 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.77 % Allowed : 12.12 % Favored : 87.12 % 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: 2.58 (0.29), residues: 894 helix: 2.07 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.21 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 399 HIS 0.005 0.001 HIS A 106 PHE 0.010 0.001 PHE A 35 TYR 0.009 0.001 TYR B 214 ARG 0.004 0.000 ARG B 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.864 Fit side-chains REVERT: A 267 PHE cc_start: 0.7917 (m-80) cc_final: 0.7630 (m-10) REVERT: A 308 LYS cc_start: 0.7875 (mttm) cc_final: 0.7639 (mttt) REVERT: A 373 GLN cc_start: 0.7744 (mt0) cc_final: 0.7455 (mt0) REVERT: A 425 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7135 (tm-30) REVERT: A 455 LEU cc_start: 0.6965 (mt) cc_final: 0.6374 (tp) REVERT: A 459 PHE cc_start: 0.6450 (t80) cc_final: 0.5799 (t80) REVERT: A 553 ASP cc_start: 0.7369 (t0) cc_final: 0.6898 (t70) REVERT: B 123 ARG cc_start: 0.5450 (ptp-110) cc_final: 0.4618 (ptp-170) REVERT: B 425 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: B 455 LEU cc_start: 0.6863 (mt) cc_final: 0.6402 (tp) REVERT: B 491 MET cc_start: 0.7529 (mtp) cc_final: 0.7096 (mtp) REVERT: B 525 MET cc_start: 0.6558 (ttm) cc_final: 0.5946 (ttt) outliers start: 6 outliers final: 2 residues processed: 127 average time/residue: 1.0026 time to fit residues: 136.3529 Evaluate side-chains 123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 425 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.0030 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.185432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140693 restraints weight = 6287.604| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.75 r_work: 0.3524 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7346 Z= 0.183 Angle : 0.560 7.259 10018 Z= 0.284 Chirality : 0.041 0.152 1212 Planarity : 0.005 0.055 1200 Dihedral : 4.243 27.081 950 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.38 % Allowed : 12.24 % Favored : 87.37 % 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: 2.60 (0.29), residues: 894 helix: 2.11 (0.19), residues: 722 sheet: None (None), residues: 0 loop : 0.11 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 399 HIS 0.005 0.001 HIS A 106 PHE 0.011 0.001 PHE A 35 TYR 0.026 0.001 TYR B 489 ARG 0.003 0.000 ARG A 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.76 seconds wall clock time: 55 minutes 3.04 seconds (3303.04 seconds total)