Starting phenix.real_space_refine on Mon Apr 28 05:31:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvh_42620/04_2025/8uvh_42620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvh_42620/04_2025/8uvh_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_42620/04_2025/8uvh_42620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvh_42620/04_2025/8uvh_42620.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvh_42620/04_2025/8uvh_42620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvh_42620/04_2025/8uvh_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.27, 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 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: 0.65 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: 1.98 Time building geometry restraints manager: 2.34 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: 0.03 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: 1.220 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.670 Find NCS groups from input model: 0.120 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:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- 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= 0.201 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 Details of bonding type rmsd hydrogen bonds : bond 0.13043 ( 512) hydrogen bonds : angle 5.05632 ( 1512) covalent geometry : bond 0.00350 ( 7346) covalent geometry : angle 0.64030 (10018) *********************** 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 : 0.801 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: 1.0621 time to fit residues: 164.8093 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 : 0.779 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.185213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140103 restraints weight = 6244.840| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.75 r_work: 0.3504 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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= 0.153 Angle : 0.575 5.938 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 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 512) hydrogen bonds : angle 4.13949 ( 1512) covalent geometry : bond 0.00342 ( 7346) covalent geometry : angle 0.57484 (10018) *********************** 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: 0.7443 (tp) cc_final: 0.7124 (pt) REVERT: A 123 ARG cc_start: 0.5198 (ptp-110) cc_final: 0.4575 (ptp-170) REVERT: A 267 PHE cc_start: 0.7754 (m-80) cc_final: 0.7497 (m-10) REVERT: A 308 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7714 (mttm) REVERT: A 425 GLU cc_start: 0.7431 (tp30) cc_final: 0.7141 (mm-30) REVERT: A 455 LEU cc_start: 0.6741 (mt) cc_final: 0.6031 (tp) REVERT: A 532 MET cc_start: 0.7384 (mmt) cc_final: 0.7167 (mmm) REVERT: A 545 ASN cc_start: 0.7933 (m-40) cc_final: 0.7506 (m110) REVERT: B 123 ARG cc_start: 0.5193 (ptp-110) cc_final: 0.4585 (ptp-170) REVERT: B 208 MET cc_start: 0.7358 (mmm) cc_final: 0.6970 (mmp) REVERT: B 261 MET cc_start: 0.8005 (tmm) cc_final: 0.7801 (tmm) REVERT: B 308 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7619 (mttp) REVERT: B 455 LEU cc_start: 0.6684 (mt) cc_final: 0.6088 (tp) REVERT: B 491 MET cc_start: 0.7566 (mtp) cc_final: 0.7048 (mtp) REVERT: B 534 ILE cc_start: 0.7264 (mt) cc_final: 0.6975 (tp) outliers start: 7 outliers final: 3 residues processed: 134 average time/residue: 1.1327 time to fit residues: 161.1121 Evaluate side-chains 124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.182486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137028 restraints weight = 6354.728| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.77 r_work: 0.3475 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7346 Z= 0.164 Angle : 0.593 6.183 10018 Z= 0.303 Chirality : 0.043 0.138 1212 Planarity : 0.006 0.055 1200 Dihedral : 4.412 22.644 950 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.89 % Allowed : 8.04 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.28), residues: 894 helix: 2.02 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.13 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 399 HIS 0.006 0.001 HIS A 106 PHE 0.017 0.001 PHE A 35 TYR 0.009 0.001 TYR B 214 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 512) hydrogen bonds : angle 4.06164 ( 1512) covalent geometry : bond 0.00384 ( 7346) covalent geometry : angle 0.59258 (10018) *********************** 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 136 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.804 Fit side-chains REVERT: A 77 GLN cc_start: 0.7729 (mt0) cc_final: 0.7528 (mt0) REVERT: A 123 ARG cc_start: 0.5210 (ptp-110) cc_final: 0.4803 (ttm110) REVERT: A 267 PHE cc_start: 0.7741 (m-80) cc_final: 0.7447 (m-10) REVERT: A 308 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7715 (mttt) REVERT: A 373 GLN cc_start: 0.7837 (mt0) cc_final: 0.7557 (mt0) REVERT: A 425 GLU cc_start: 0.7399 (tp30) cc_final: 0.7157 (mp0) REVERT: A 455 LEU cc_start: 0.6753 (mt) cc_final: 0.6043 (tp) REVERT: A 459 PHE cc_start: 0.6293 (t80) cc_final: 0.5757 (t80) REVERT: A 532 MET cc_start: 0.7452 (mmt) cc_final: 0.7241 (mmm) REVERT: A 553 ASP cc_start: 0.7711 (t0) cc_final: 0.7111 (t70) REVERT: B 52 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6906 (mt-10) REVERT: B 123 ARG cc_start: 0.5261 (ptp-110) cc_final: 0.4597 (ptp-170) REVERT: B 208 MET cc_start: 0.7414 (mmm) cc_final: 0.7007 (mmp) REVERT: B 261 MET cc_start: 0.8036 (tmm) cc_final: 0.7746 (tmm) REVERT: B 308 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7712 (mttp) REVERT: B 425 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: B 455 LEU cc_start: 0.6665 (mt) cc_final: 0.6169 (tp) REVERT: B 491 MET cc_start: 0.7651 (mtp) cc_final: 0.7131 (mtp) outliers start: 7 outliers final: 3 residues processed: 129 average time/residue: 1.0501 time to fit residues: 144.2668 Evaluate side-chains 124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 425 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.189156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144595 restraints weight = 6228.371| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.83 r_work: 0.3578 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1617 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= 0.140 Angle : 0.556 6.085 10018 Z= 0.286 Chirality : 0.041 0.147 1212 Planarity : 0.006 0.055 1200 Dihedral : 4.351 28.228 950 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.28 % Allowed : 9.18 % Favored : 89.54 % 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: 2.45 (0.28), residues: 894 helix: 2.04 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -0.09 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 399 HIS 0.005 0.001 HIS B 106 PHE 0.013 0.001 PHE A 35 TYR 0.008 0.001 TYR A 48 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 512) hydrogen bonds : angle 3.97013 ( 1512) covalent geometry : bond 0.00325 ( 7346) covalent geometry : angle 0.55567 (10018) *********************** 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 139 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.199 Fit side-chains REVERT: A 123 ARG cc_start: 0.5170 (ptp-110) cc_final: 0.4785 (ttm110) REVERT: A 267 PHE cc_start: 0.7693 (m-80) cc_final: 0.7369 (m-10) REVERT: A 308 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7675 (mttt) REVERT: A 373 GLN cc_start: 0.7816 (mt0) cc_final: 0.7495 (mt0) REVERT: A 425 GLU cc_start: 0.7294 (tp30) cc_final: 0.7029 (mp0) REVERT: A 455 LEU cc_start: 0.6776 (mt) cc_final: 0.6088 (tp) REVERT: A 459 PHE cc_start: 0.6304 (t80) cc_final: 0.5743 (t80) REVERT: A 532 MET cc_start: 0.7404 (mmt) cc_final: 0.7161 (mmm) REVERT: A 553 ASP cc_start: 0.7699 (t0) cc_final: 0.7085 (t70) REVERT: B 52 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6922 (mt-10) REVERT: B 123 ARG cc_start: 0.5304 (ptp-110) cc_final: 0.4483 (ptp-170) REVERT: B 261 MET cc_start: 0.7947 (tmm) cc_final: 0.7664 (tmm) REVERT: B 425 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: B 455 LEU cc_start: 0.6631 (mt) cc_final: 0.6123 (tp) REVERT: B 491 MET cc_start: 0.7461 (mtp) cc_final: 0.6950 (mtp) outliers start: 10 outliers final: 3 residues processed: 129 average time/residue: 1.0215 time to fit residues: 140.9837 Evaluate side-chains 123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.183570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138515 restraints weight = 6291.419| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.74 r_work: 0.3498 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1680 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= 0.137 Angle : 0.554 6.072 10018 Z= 0.283 Chirality : 0.041 0.145 1212 Planarity : 0.006 0.055 1200 Dihedral : 4.299 27.295 950 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.15 % Allowed : 9.82 % Favored : 89.03 % 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: 2.46 (0.28), residues: 894 helix: 2.03 (0.19), 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 0.005 0.001 HIS A 106 PHE 0.013 0.001 PHE A 35 TYR 0.015 0.001 TYR B 489 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 512) hydrogen bonds : angle 3.93928 ( 1512) covalent geometry : bond 0.00316 ( 7346) covalent geometry : angle 0.55381 (10018) *********************** 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 136 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.726 Fit side-chains REVERT: A 123 ARG cc_start: 0.5224 (ptp-110) cc_final: 0.4960 (ttm110) REVERT: A 308 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7711 (mttt) REVERT: A 373 GLN cc_start: 0.7853 (mt0) cc_final: 0.7541 (mt0) REVERT: A 425 GLU cc_start: 0.7312 (tp30) cc_final: 0.7074 (mp0) REVERT: A 455 LEU cc_start: 0.6831 (mt) cc_final: 0.6154 (tp) REVERT: A 459 PHE cc_start: 0.6461 (t80) cc_final: 0.5871 (t80) REVERT: A 532 MET cc_start: 0.7454 (mmt) cc_final: 0.7191 (mmm) REVERT: A 553 ASP cc_start: 0.7743 (t0) cc_final: 0.7162 (t70) REVERT: B 52 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6843 (mt-10) REVERT: B 123 ARG cc_start: 0.5327 (ptp-110) cc_final: 0.4510 (ptp-170) REVERT: B 261 MET cc_start: 0.8050 (tmm) cc_final: 0.7827 (tmm) REVERT: B 425 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 455 LEU cc_start: 0.6697 (mt) cc_final: 0.6200 (tp) REVERT: B 491 MET cc_start: 0.7556 (mtp) cc_final: 0.7048 (mtp) outliers start: 9 outliers final: 4 residues processed: 127 average time/residue: 0.9684 time to fit residues: 131.2009 Evaluate side-chains 124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 142 THR 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 43 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.184686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.140155 restraints weight = 6285.012| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.74 r_work: 0.3514 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1779 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= 0.124 Angle : 0.536 5.821 10018 Z= 0.274 Chirality : 0.040 0.139 1212 Planarity : 0.005 0.055 1200 Dihedral : 4.254 26.749 950 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.02 % Allowed : 10.33 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.28), residues: 894 helix: 2.12 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.07 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 399 HIS 0.004 0.001 HIS A 106 PHE 0.011 0.001 PHE A 35 TYR 0.008 0.001 TYR A 48 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 512) hydrogen bonds : angle 3.87729 ( 1512) covalent geometry : bond 0.00280 ( 7346) covalent geometry : angle 0.53551 (10018) *********************** 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: 8 poor density : 126 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 123 ARG cc_start: 0.5257 (ptp-110) cc_final: 0.4998 (ttm110) REVERT: A 267 PHE cc_start: 0.7761 (m-80) cc_final: 0.7510 (m-10) REVERT: A 373 GLN cc_start: 0.7877 (mt0) cc_final: 0.7562 (mt0) REVERT: A 425 GLU cc_start: 0.7363 (tp30) cc_final: 0.7149 (mp0) REVERT: A 455 LEU cc_start: 0.6840 (mt) cc_final: 0.6186 (tp) REVERT: A 459 PHE cc_start: 0.6461 (t80) cc_final: 0.5869 (t80) REVERT: A 532 MET cc_start: 0.7420 (mmt) cc_final: 0.7159 (mmm) REVERT: A 553 ASP cc_start: 0.7731 (t0) cc_final: 0.7155 (t70) REVERT: B 52 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6801 (mt-10) REVERT: B 123 ARG cc_start: 0.5327 (ptp-110) cc_final: 0.4513 (ptp-170) REVERT: B 261 MET cc_start: 0.7987 (tmm) cc_final: 0.7772 (tmm) REVERT: B 425 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: B 455 LEU cc_start: 0.6627 (mt) cc_final: 0.6136 (tp) REVERT: B 491 MET cc_start: 0.7535 (mtp) cc_final: 0.7112 (mtp) REVERT: B 525 MET cc_start: 0.6098 (ttm) cc_final: 0.5514 (ttt) outliers start: 8 outliers final: 3 residues processed: 126 average time/residue: 1.0748 time to fit residues: 144.8204 Evaluate side-chains 124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 425 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 533 ASN B 71 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.179275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133658 restraints weight = 6292.110| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.77 r_work: 0.3440 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.006 0.049 7346 Z= 0.228 Angle : 0.673 7.686 10018 Z= 0.341 Chirality : 0.046 0.143 1212 Planarity : 0.006 0.059 1200 Dihedral : 4.569 26.706 950 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.28 % Allowed : 10.71 % 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: 2.09 (0.28), residues: 894 helix: 1.74 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -0.05 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 103 HIS 0.011 0.002 HIS A 106 PHE 0.023 0.002 PHE A 35 TYR 0.015 0.002 TYR B 489 ARG 0.005 0.001 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 512) hydrogen bonds : angle 4.22226 ( 1512) covalent geometry : bond 0.00553 ( 7346) covalent geometry : angle 0.67252 (10018) *********************** 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 133 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.821 Fit side-chains REVERT: A 308 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7676 (mttt) REVERT: A 373 GLN cc_start: 0.7920 (mt0) cc_final: 0.7625 (mt0) REVERT: A 455 LEU cc_start: 0.6840 (mt) cc_final: 0.6194 (tp) REVERT: A 459 PHE cc_start: 0.6539 (t80) cc_final: 0.5704 (t80) REVERT: A 532 MET cc_start: 0.7486 (mmt) cc_final: 0.7217 (mmm) REVERT: A 553 ASP cc_start: 0.7839 (t0) cc_final: 0.7259 (t70) REVERT: B 112 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6733 (tpm170) REVERT: B 123 ARG cc_start: 0.5374 (ptp-110) cc_final: 0.4534 (ptp-170) REVERT: B 261 MET cc_start: 0.8152 (tmm) cc_final: 0.7863 (tmm) REVERT: B 308 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7647 (mttp) REVERT: B 425 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: B 455 LEU cc_start: 0.6728 (mt) cc_final: 0.6261 (tp) REVERT: B 491 MET cc_start: 0.7812 (mtp) cc_final: 0.7325 (mtp) outliers start: 10 outliers final: 3 residues processed: 124 average time/residue: 1.0343 time to fit residues: 136.7133 Evaluate side-chains 124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 112 ARG Chi-restraints excluded: chain B residue 142 THR 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 59 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.181275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136564 restraints weight = 6322.721| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.72 r_work: 0.3476 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7346 Z= 0.156 Angle : 0.588 6.715 10018 Z= 0.300 Chirality : 0.042 0.145 1212 Planarity : 0.006 0.057 1200 Dihedral : 4.453 26.447 950 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.28 % Allowed : 10.97 % Favored : 87.76 % 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: 2.27 (0.28), residues: 894 helix: 1.87 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.02 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 399 HIS 0.007 0.001 HIS A 106 PHE 0.014 0.001 PHE A 35 TYR 0.009 0.001 TYR B 214 ARG 0.002 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 512) hydrogen bonds : angle 4.05112 ( 1512) covalent geometry : bond 0.00370 ( 7346) covalent geometry : angle 0.58770 (10018) *********************** 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 134 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.782 Fit side-chains REVERT: A 308 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7619 (mttt) REVERT: A 373 GLN cc_start: 0.7899 (mt0) cc_final: 0.7601 (mt0) REVERT: A 425 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: A 455 LEU cc_start: 0.6834 (mt) cc_final: 0.6204 (tp) REVERT: A 459 PHE cc_start: 0.6488 (t80) cc_final: 0.5621 (t80) REVERT: A 532 MET cc_start: 0.7413 (mmt) cc_final: 0.7120 (mmm) REVERT: A 553 ASP cc_start: 0.7796 (t0) cc_final: 0.7211 (t70) REVERT: B 112 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6572 (tpm170) REVERT: B 123 ARG cc_start: 0.5416 (ptp-110) cc_final: 0.4604 (ptp-170) REVERT: B 261 MET cc_start: 0.8095 (tmm) cc_final: 0.7806 (tmm) REVERT: B 308 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7610 (mttp) REVERT: B 425 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: B 455 LEU cc_start: 0.6698 (mt) cc_final: 0.6214 (tp) REVERT: B 491 MET cc_start: 0.7614 (mtp) cc_final: 0.7205 (mtp) outliers start: 10 outliers final: 5 residues processed: 125 average time/residue: 1.0196 time to fit residues: 136.0338 Evaluate side-chains 126 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 425 GLU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 112 ARG 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 82 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.179713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134751 restraints weight = 6414.059| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.73 r_work: 0.3455 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7346 Z= 0.199 Angle : 0.638 6.975 10018 Z= 0.324 Chirality : 0.044 0.148 1212 Planarity : 0.006 0.058 1200 Dihedral : 4.539 26.395 950 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.15 % Allowed : 11.61 % Favored : 87.24 % 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: 2.14 (0.28), residues: 894 helix: 1.77 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.03 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 399 HIS 0.010 0.002 HIS A 106 PHE 0.019 0.002 PHE A 35 TYR 0.011 0.001 TYR B 214 ARG 0.003 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 512) hydrogen bonds : angle 4.16004 ( 1512) covalent geometry : bond 0.00481 ( 7346) covalent geometry : angle 0.63789 (10018) *********************** 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 132 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.7876 (mt0) cc_final: 0.7578 (mt0) REVERT: A 425 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7395 (tp30) REVERT: A 455 LEU cc_start: 0.6819 (mt) cc_final: 0.6181 (tp) REVERT: A 459 PHE cc_start: 0.6504 (t80) cc_final: 0.5625 (t80) REVERT: A 532 MET cc_start: 0.7410 (mmt) cc_final: 0.7105 (mmm) REVERT: A 553 ASP cc_start: 0.7844 (t0) cc_final: 0.7246 (t70) REVERT: B 112 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6531 (tpm170) REVERT: B 123 ARG cc_start: 0.5405 (ptp-110) cc_final: 0.4586 (ptp-170) REVERT: B 261 MET cc_start: 0.8053 (tmm) cc_final: 0.7771 (tmm) REVERT: B 308 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7572 (mttp) REVERT: B 425 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: B 455 LEU cc_start: 0.6664 (mt) cc_final: 0.6203 (tp) REVERT: B 491 MET cc_start: 0.7682 (mtp) cc_final: 0.7178 (mtp) outliers start: 9 outliers final: 5 residues processed: 124 average time/residue: 1.0397 time to fit residues: 137.9417 Evaluate side-chains 127 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 425 GLU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 112 ARG 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 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 77 GLN B 104 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.182944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137809 restraints weight = 6446.234| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.74 r_work: 0.3493 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2076 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= 0.133 Angle : 0.571 6.679 10018 Z= 0.291 Chirality : 0.041 0.141 1212 Planarity : 0.006 0.057 1200 Dihedral : 4.407 26.236 950 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.02 % Allowed : 11.73 % Favored : 87.24 % 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: 2.37 (0.29), residues: 894 helix: 1.94 (0.20), residues: 726 sheet: None (None), residues: 0 loop : 0.06 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 399 HIS 0.006 0.001 HIS A 106 PHE 0.011 0.001 PHE A 35 TYR 0.011 0.001 TYR A 48 ARG 0.005 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 512) hydrogen bonds : angle 3.98990 ( 1512) covalent geometry : bond 0.00304 ( 7346) covalent geometry : angle 0.57088 (10018) ********************** 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 133 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.751 Fit side-chains REVERT: A 267 PHE cc_start: 0.7793 (m-80) cc_final: 0.7519 (m-10) REVERT: A 308 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7592 (mttt) REVERT: A 373 GLN cc_start: 0.7887 (mt0) cc_final: 0.7588 (mt0) REVERT: A 425 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: A 455 LEU cc_start: 0.6814 (mt) cc_final: 0.6182 (tp) REVERT: A 459 PHE cc_start: 0.6486 (t80) cc_final: 0.5835 (t80) REVERT: A 532 MET cc_start: 0.7403 (mmt) cc_final: 0.7090 (mmm) REVERT: A 553 ASP cc_start: 0.7815 (t0) cc_final: 0.7219 (t70) REVERT: B 123 ARG cc_start: 0.5402 (ptp-110) cc_final: 0.4584 (ptp-170) REVERT: B 308 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7594 (mttp) REVERT: B 425 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: B 455 LEU cc_start: 0.6717 (mt) cc_final: 0.6210 (tp) REVERT: B 491 MET cc_start: 0.7538 (mtp) cc_final: 0.7036 (mtp) REVERT: B 525 MET cc_start: 0.6009 (ttm) cc_final: 0.5407 (ttt) outliers start: 8 outliers final: 3 residues processed: 126 average time/residue: 1.0972 time to fit residues: 149.3874 Evaluate side-chains 125 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 425 GLU 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 51 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 78 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.183347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138351 restraints weight = 6288.342| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.73 r_work: 0.3500 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2071 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= 0.133 Angle : 0.565 7.114 10018 Z= 0.288 Chirality : 0.041 0.142 1212 Planarity : 0.005 0.057 1200 Dihedral : 4.368 26.127 950 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.89 % Allowed : 11.99 % 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: 2.41 (0.29), residues: 894 helix: 1.97 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.06 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 399 HIS 0.006 0.001 HIS A 106 PHE 0.011 0.001 PHE A 35 TYR 0.011 0.001 TYR B 48 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 512) hydrogen bonds : angle 3.96650 ( 1512) covalent geometry : bond 0.00306 ( 7346) covalent geometry : angle 0.56528 (10018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7502.27 seconds wall clock time: 130 minutes 6.47 seconds (7806.47 seconds total)