Starting phenix.real_space_refine on Tue Feb 3 15:36:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nbw_49237/02_2026/9nbw_49237_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nbw_49237/02_2026/9nbw_49237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nbw_49237/02_2026/9nbw_49237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nbw_49237/02_2026/9nbw_49237.map" model { file = "/net/cci-nas-00/data/ceres_data/9nbw_49237/02_2026/9nbw_49237_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nbw_49237/02_2026/9nbw_49237_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 7 Type Number sf(0) Gaussians As 1 7.32 5 P 6 5.49 5 Mg 2 5.21 5 S 13 5.16 5 C 2736 2.51 5 N 778 2.21 5 O 851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4387 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4309 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 33, 'TRANS': 536} Chain breaks: 2 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 78 Unusual residues: {' MG': 2, 'ARS': 1, 'ATP': 2} Classifications: {'undetermined': 5, 'water': 13} Link IDs: {None: 17} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 825 SG CYS A 114 28.509 30.458 24.844 1.00 79.97 S ATOM 1268 SG CYS A 173 30.665 31.373 21.160 1.00102.53 S ATOM 3074 SG CYS A 422 31.246 32.395 24.259 1.00 91.63 S Time building chain proxies: 1.17, per 1000 atoms: 0.27 Number of scatterers: 4387 At special positions: 0 Unit cell: (59.15, 74.1, 88.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) As 1 32.98 S 13 16.00 P 6 15.00 Mg 2 11.99 O 851 8.00 N 778 7.00 C 2736 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 333.9 milliseconds 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 58.6% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 112 through 130 removed outlier: 3.707A pdb=" N THR A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 166 removed outlier: 4.377A pdb=" N ARG A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 209 through 227 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.647A pdb=" N ALA A 245 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 263 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 315 through 326 removed outlier: 3.785A pdb=" N ASP A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.555A pdb=" N THR A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 402 Processing helix chain 'A' and resid 407 through 419 Processing helix chain 'A' and resid 422 through 437 removed outlier: 3.831A pdb=" N ILE A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 441 removed outlier: 3.872A pdb=" N LYS A 441 " --> pdb=" O GLU A 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.796A pdb=" N LEU A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.554A pdb=" N GLN A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'A' and resid 538 through 558 removed outlier: 4.272A pdb=" N ARG A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 removed outlier: 4.219A pdb=" N ARG A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 584 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.561A pdb=" N LEU A 41 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASP A 143 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 43 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N MET A 12 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 11 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL A 203 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A 13 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 205 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR A 15 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ARG A 207 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N HIS A 232 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 202 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL A 234 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 204 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN A 236 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA A 206 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE A 238 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.804A pdb=" N VAL A 358 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 329 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 495 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET A 331 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 497 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET A 333 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 524 " --> pdb=" O VAL A 494 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1488 1.34 - 1.46: 438 1.46 - 1.57: 2491 1.57 - 1.69: 10 1.69 - 1.81: 22 Bond restraints: 4449 Sorted by residual: bond pdb=" C1' ATP A 601 " pdb=" O4' ATP A 601 " ideal model delta sigma weight residual 1.416 1.400 0.016 1.30e-02 5.92e+03 1.45e+00 bond pdb=" C4' ATP A 602 " pdb=" O4' ATP A 602 " ideal model delta sigma weight residual 1.444 1.432 0.012 1.10e-02 8.26e+03 1.13e+00 bond pdb=" C1' ATP A 602 " pdb=" O4' ATP A 602 " ideal model delta sigma weight residual 1.416 1.403 0.013 1.30e-02 5.92e+03 9.91e-01 bond pdb=" C4' ATP A 601 " pdb=" O4' ATP A 601 " ideal model delta sigma weight residual 1.444 1.434 0.010 1.10e-02 8.26e+03 7.51e-01 bond pdb=" C THR A 503 " pdb=" O THR A 503 " ideal model delta sigma weight residual 1.244 1.237 0.007 9.80e-03 1.04e+04 4.80e-01 ... (remaining 4444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 5940 1.43 - 2.85: 78 2.85 - 4.28: 36 4.28 - 5.70: 11 5.70 - 7.13: 5 Bond angle restraints: 6070 Sorted by residual: angle pdb=" N ALA A 171 " pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 109.59 102.46 7.13 1.47e+00 4.63e-01 2.35e+01 angle pdb=" N SER A 172 " pdb=" CA SER A 172 " pdb=" C SER A 172 " ideal model delta sigma weight residual 112.89 107.58 5.31 1.24e+00 6.50e-01 1.83e+01 angle pdb=" C ALA A 171 " pdb=" CA ALA A 171 " pdb=" CB ALA A 171 " ideal model delta sigma weight residual 110.26 115.73 -5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C ASN A 528 " pdb=" CA ASN A 528 " pdb=" CB ASN A 528 " ideal model delta sigma weight residual 109.51 104.41 5.10 1.71e+00 3.42e-01 8.91e+00 angle pdb=" C ALA A 245 " pdb=" CA ALA A 245 " pdb=" CB ALA A 245 " ideal model delta sigma weight residual 109.65 104.74 4.91 1.71e+00 3.42e-01 8.24e+00 ... (remaining 6065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2504 16.15 - 32.29: 180 32.29 - 48.44: 32 48.44 - 64.59: 25 64.59 - 80.73: 5 Dihedral angle restraints: 2746 sinusoidal: 1113 harmonic: 1633 Sorted by residual: dihedral pdb=" CA MET A 446 " pdb=" C MET A 446 " pdb=" N ASP A 447 " pdb=" CA ASP A 447 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CB MET A 2 " pdb=" CG MET A 2 " pdb=" SD MET A 2 " pdb=" CE MET A 2 " ideal model delta sinusoidal sigma weight residual 180.00 122.81 57.19 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N THR A 147 " pdb=" CA THR A 147 " ideal model delta harmonic sigma weight residual -180.00 -164.67 -15.33 0 5.00e+00 4.00e-02 9.40e+00 ... (remaining 2743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 615 0.055 - 0.109: 84 0.109 - 0.164: 19 0.164 - 0.218: 1 0.218 - 0.273: 6 Chirality restraints: 725 Sorted by residual: chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ATP A 601 " pdb=" C2' ATP A 601 " pdb=" C4' ATP A 601 " pdb=" O3' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ATP A 602 " pdb=" C2' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" O3' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 722 not shown) Planarity restraints: 782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 8 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 9 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 392 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C GLU A 392 " 0.019 2.00e-02 2.50e+03 pdb=" O GLU A 392 " -0.007 2.00e-02 2.50e+03 pdb=" N ARG A 393 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 145 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 146 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.015 5.00e-02 4.00e+02 ... (remaining 779 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 13 2.42 - 3.04: 2855 3.04 - 3.66: 6566 3.66 - 4.28: 10028 4.28 - 4.90: 17157 Nonbonded interactions: 36619 Sorted by model distance: nonbonded pdb="MG MG A 604 " pdb=" O HOH A 702 " model vdw 1.803 2.170 nonbonded pdb="MG MG A 604 " pdb=" O HOH A 706 " model vdw 1.805 2.170 nonbonded pdb="MG MG A 603 " pdb=" O HOH A 701 " model vdw 1.806 2.170 nonbonded pdb=" OG1 THR A 23 " pdb="MG MG A 604 " model vdw 1.838 2.170 nonbonded pdb="MG MG A 603 " pdb=" O HOH A 705 " model vdw 1.843 2.170 ... (remaining 36614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.860 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.920 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 0.243 4450 Z= 0.378 Angle : 0.561 7.128 6070 Z= 0.295 Chirality : 0.048 0.273 725 Planarity : 0.004 0.036 782 Dihedral : 13.564 80.732 1686 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.37), residues: 564 helix: 1.87 (0.32), residues: 289 sheet: -2.18 (0.54), residues: 82 loop : -0.26 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 218 TYR 0.005 0.001 TYR A 86 PHE 0.016 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.000 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4449) covalent geometry : angle 0.56077 ( 6070) hydrogen bonds : bond 0.11427 ( 231) hydrogen bonds : angle 4.97715 ( 669) Misc. bond : bond 0.24305 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.181 Fit side-chains REVERT: A 38 LYS cc_start: 0.8014 (mppt) cc_final: 0.7212 (mmtt) REVERT: A 39 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7374 (mtp85) REVERT: A 62 ARG cc_start: 0.7353 (ptt90) cc_final: 0.6989 (ptt-90) REVERT: A 88 GLU cc_start: 0.7474 (tp30) cc_final: 0.6603 (OUTLIER) REVERT: A 215 GLU cc_start: 0.8405 (tp30) cc_final: 0.8188 (tp30) REVERT: A 425 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 510 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7439 (ttpp) REVERT: A 571 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6779 (pm20) outliers start: 0 outliers final: 2 residues processed: 79 average time/residue: 0.6354 time to fit residues: 51.5561 Evaluate side-chains 46 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 258 GLN A 263 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.141361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.106640 restraints weight = 4213.250| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.93 r_work: 0.3010 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4450 Z= 0.140 Angle : 0.527 7.538 6070 Z= 0.269 Chirality : 0.043 0.140 725 Planarity : 0.005 0.050 782 Dihedral : 8.849 80.830 677 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.32 % Allowed : 9.93 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.37), residues: 564 helix: 1.86 (0.31), residues: 293 sheet: -1.92 (0.54), residues: 82 loop : -0.22 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.004 0.001 TYR A 563 PHE 0.019 0.002 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4449) covalent geometry : angle 0.52652 ( 6070) hydrogen bonds : bond 0.03393 ( 231) hydrogen bonds : angle 3.87597 ( 669) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.161 Fit side-chains REVERT: A 38 LYS cc_start: 0.8128 (mppt) cc_final: 0.7310 (mmtt) REVERT: A 39 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7434 (mtp85) REVERT: A 62 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7092 (ptt-90) REVERT: A 90 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7569 (mm) REVERT: A 425 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 466 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7818 (ttp-110) REVERT: A 492 THR cc_start: 0.8919 (t) cc_final: 0.8607 (m) REVERT: A 510 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7685 (ttpp) REVERT: A 550 ARG cc_start: 0.7663 (ptp-170) cc_final: 0.7021 (mtm110) REVERT: A 571 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6785 (pm20) outliers start: 6 outliers final: 0 residues processed: 55 average time/residue: 0.5762 time to fit residues: 32.8053 Evaluate side-chains 47 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125659 restraints weight = 3991.321| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.84 r_work: 0.3100 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4450 Z= 0.143 Angle : 0.509 6.793 6070 Z= 0.258 Chirality : 0.042 0.134 725 Planarity : 0.005 0.058 782 Dihedral : 8.924 78.228 675 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.99 % Allowed : 10.15 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.36), residues: 564 helix: 1.96 (0.31), residues: 288 sheet: -1.87 (0.52), residues: 87 loop : -0.16 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.007 0.001 TYR A 137 PHE 0.016 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4449) covalent geometry : angle 0.50904 ( 6070) hydrogen bonds : bond 0.03132 ( 231) hydrogen bonds : angle 3.78495 ( 669) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.100 Fit side-chains REVERT: A 38 LYS cc_start: 0.8107 (mppt) cc_final: 0.7290 (mmtt) REVERT: A 39 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7446 (mtp85) REVERT: A 62 ARG cc_start: 0.7518 (ptt90) cc_final: 0.6967 (ptt-90) REVERT: A 88 GLU cc_start: 0.7626 (tp30) cc_final: 0.6931 (mp0) REVERT: A 90 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7660 (mm) REVERT: A 425 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 466 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7827 (ttp-110) REVERT: A 492 THR cc_start: 0.8890 (t) cc_final: 0.8600 (m) REVERT: A 510 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7594 (ttpp) REVERT: A 571 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6811 (pm20) outliers start: 9 outliers final: 3 residues processed: 57 average time/residue: 0.7141 time to fit residues: 41.8970 Evaluate side-chains 49 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 570 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.158954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126959 restraints weight = 3887.612| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.76 r_work: 0.3070 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4450 Z= 0.141 Angle : 0.501 6.293 6070 Z= 0.255 Chirality : 0.042 0.134 725 Planarity : 0.005 0.060 782 Dihedral : 9.035 76.663 675 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.77 % Allowed : 12.80 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.36), residues: 564 helix: 1.97 (0.31), residues: 288 sheet: -1.91 (0.50), residues: 89 loop : -0.10 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.007 0.001 TYR A 86 PHE 0.016 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4449) covalent geometry : angle 0.50072 ( 6070) hydrogen bonds : bond 0.03068 ( 231) hydrogen bonds : angle 3.71887 ( 669) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.103 Fit side-chains REVERT: A 38 LYS cc_start: 0.8067 (mppt) cc_final: 0.7237 (mmtt) REVERT: A 39 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7459 (mtp85) REVERT: A 62 ARG cc_start: 0.7480 (ptt90) cc_final: 0.6966 (ptt-90) REVERT: A 88 GLU cc_start: 0.7605 (tp30) cc_final: 0.6854 (mp0) REVERT: A 90 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7613 (mm) REVERT: A 425 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 472 MET cc_start: 0.7419 (mpp) cc_final: 0.7051 (mmt) REVERT: A 492 THR cc_start: 0.8858 (t) cc_final: 0.8571 (m) REVERT: A 510 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7631 (ttpp) REVERT: A 571 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6766 (pm20) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.6137 time to fit residues: 34.1615 Evaluate side-chains 55 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 570 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.0020 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.142090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107391 restraints weight = 4125.617| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.86 r_work: 0.3123 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4450 Z= 0.116 Angle : 0.475 5.556 6070 Z= 0.244 Chirality : 0.041 0.132 725 Planarity : 0.005 0.060 782 Dihedral : 8.937 79.579 675 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.77 % Allowed : 13.25 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.36), residues: 564 helix: 1.86 (0.31), residues: 300 sheet: -1.77 (0.51), residues: 88 loop : -0.08 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.008 0.001 TYR A 137 PHE 0.016 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4449) covalent geometry : angle 0.47465 ( 6070) hydrogen bonds : bond 0.02792 ( 231) hydrogen bonds : angle 3.62629 ( 669) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.163 Fit side-chains REVERT: A 38 LYS cc_start: 0.8078 (mppt) cc_final: 0.7255 (mmtt) REVERT: A 39 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7502 (mtp85) REVERT: A 62 ARG cc_start: 0.7469 (ptt90) cc_final: 0.6945 (ptt-90) REVERT: A 88 GLU cc_start: 0.7658 (tp30) cc_final: 0.6941 (mp0) REVERT: A 90 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7626 (mm) REVERT: A 425 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 466 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7843 (ttp-110) REVERT: A 472 MET cc_start: 0.7534 (mpp) cc_final: 0.6934 (mmt) REVERT: A 492 THR cc_start: 0.8852 (t) cc_final: 0.8575 (m) REVERT: A 510 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7703 (ttpp) REVERT: A 571 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6711 (pm20) outliers start: 8 outliers final: 3 residues processed: 55 average time/residue: 0.5464 time to fit residues: 30.9662 Evaluate side-chains 52 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 570 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117447 restraints weight = 4128.092| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.98 r_work: 0.3167 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4450 Z= 0.193 Angle : 0.548 8.056 6070 Z= 0.276 Chirality : 0.044 0.144 725 Planarity : 0.006 0.064 782 Dihedral : 9.580 68.125 675 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.36), residues: 564 helix: 1.67 (0.30), residues: 295 sheet: -1.75 (0.52), residues: 82 loop : -0.18 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 470 TYR 0.007 0.001 TYR A 86 PHE 0.015 0.002 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 4449) covalent geometry : angle 0.54835 ( 6070) hydrogen bonds : bond 0.03475 ( 231) hydrogen bonds : angle 3.85886 ( 669) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.097 Fit side-chains REVERT: A 38 LYS cc_start: 0.8039 (mppt) cc_final: 0.7189 (mmtt) REVERT: A 39 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7429 (mtp85) REVERT: A 62 ARG cc_start: 0.7393 (ptt90) cc_final: 0.6811 (ptt-90) REVERT: A 90 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7559 (mm) REVERT: A 425 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7311 (mm-30) REVERT: A 466 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7691 (ttp-110) REVERT: A 472 MET cc_start: 0.7412 (mpp) cc_final: 0.6894 (mmt) REVERT: A 492 THR cc_start: 0.8865 (t) cc_final: 0.8566 (m) REVERT: A 510 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7510 (ttpp) REVERT: A 548 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7204 (mp0) REVERT: A 571 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7079 (pt0) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.5297 time to fit residues: 29.5363 Evaluate side-chains 54 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 582 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126630 restraints weight = 3931.050| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.77 r_work: 0.3144 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4450 Z= 0.133 Angle : 0.503 7.111 6070 Z= 0.257 Chirality : 0.042 0.133 725 Planarity : 0.005 0.063 782 Dihedral : 9.328 72.160 675 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.55 % Allowed : 14.57 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.36), residues: 564 helix: 1.74 (0.30), residues: 300 sheet: -1.72 (0.52), residues: 82 loop : -0.22 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 470 TYR 0.009 0.001 TYR A 137 PHE 0.015 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.001 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4449) covalent geometry : angle 0.50296 ( 6070) hydrogen bonds : bond 0.02948 ( 231) hydrogen bonds : angle 3.71538 ( 669) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.114 Fit side-chains REVERT: A 38 LYS cc_start: 0.8087 (mppt) cc_final: 0.7301 (mmtt) REVERT: A 39 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7445 (mtm110) REVERT: A 62 ARG cc_start: 0.7443 (ptt90) cc_final: 0.6905 (ptt-90) REVERT: A 88 GLU cc_start: 0.7629 (tp30) cc_final: 0.6997 (mp0) REVERT: A 90 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7703 (mm) REVERT: A 325 ASP cc_start: 0.7778 (t70) cc_final: 0.7359 (t0) REVERT: A 425 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 466 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7862 (ttp-110) REVERT: A 472 MET cc_start: 0.7581 (mpp) cc_final: 0.7218 (mmt) REVERT: A 492 THR cc_start: 0.8869 (t) cc_final: 0.8586 (m) REVERT: A 510 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7692 (ttpp) REVERT: A 571 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6823 (pm20) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.5107 time to fit residues: 28.9755 Evaluate side-chains 53 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 582 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.157972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125906 restraints weight = 3949.473| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.76 r_work: 0.3163 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4450 Z= 0.155 Angle : 0.521 7.504 6070 Z= 0.264 Chirality : 0.043 0.155 725 Planarity : 0.006 0.063 782 Dihedral : 9.453 70.297 675 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.99 % Allowed : 13.69 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.36), residues: 564 helix: 1.65 (0.30), residues: 301 sheet: -1.64 (0.52), residues: 82 loop : -0.20 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 470 TYR 0.006 0.001 TYR A 86 PHE 0.015 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.001 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4449) covalent geometry : angle 0.52092 ( 6070) hydrogen bonds : bond 0.03115 ( 231) hydrogen bonds : angle 3.76101 ( 669) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.171 Fit side-chains REVERT: A 38 LYS cc_start: 0.8091 (mppt) cc_final: 0.7338 (mmtt) REVERT: A 39 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7454 (mtm110) REVERT: A 62 ARG cc_start: 0.7473 (ptt90) cc_final: 0.6920 (ptt-90) REVERT: A 88 GLU cc_start: 0.7653 (tp30) cc_final: 0.6981 (mp0) REVERT: A 90 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 325 ASP cc_start: 0.7808 (t70) cc_final: 0.7375 (t0) REVERT: A 425 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 466 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7870 (ttp-110) REVERT: A 472 MET cc_start: 0.7607 (mpp) cc_final: 0.7245 (mmm) REVERT: A 492 THR cc_start: 0.8884 (t) cc_final: 0.8605 (m) REVERT: A 510 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7710 (ttpp) REVERT: A 571 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6858 (pm20) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.5678 time to fit residues: 32.2251 Evaluate side-chains 53 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 582 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130362 restraints weight = 4024.693| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.87 r_work: 0.3197 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4450 Z= 0.114 Angle : 0.492 6.832 6070 Z= 0.252 Chirality : 0.042 0.193 725 Planarity : 0.005 0.061 782 Dihedral : 9.119 75.063 675 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.55 % Allowed : 13.91 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.36), residues: 564 helix: 1.84 (0.31), residues: 300 sheet: -1.53 (0.53), residues: 82 loop : -0.16 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 470 TYR 0.009 0.001 TYR A 137 PHE 0.015 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4449) covalent geometry : angle 0.49167 ( 6070) hydrogen bonds : bond 0.02773 ( 231) hydrogen bonds : angle 3.64948 ( 669) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.099 Fit side-chains REVERT: A 38 LYS cc_start: 0.8108 (mppt) cc_final: 0.7355 (mmtt) REVERT: A 39 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7477 (mtm110) REVERT: A 62 ARG cc_start: 0.7423 (ptt90) cc_final: 0.6918 (ptt-90) REVERT: A 88 GLU cc_start: 0.7658 (tp30) cc_final: 0.7049 (mp0) REVERT: A 90 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7817 (mm) REVERT: A 325 ASP cc_start: 0.7811 (t70) cc_final: 0.7398 (t0) REVERT: A 425 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 472 MET cc_start: 0.7657 (mpp) cc_final: 0.7071 (mmt) REVERT: A 492 THR cc_start: 0.8845 (t) cc_final: 0.8593 (m) REVERT: A 510 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7706 (ttpp) REVERT: A 571 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6821 (pm20) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.4949 time to fit residues: 28.0985 Evaluate side-chains 51 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 436 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125178 restraints weight = 3950.061| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.82 r_work: 0.3150 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4450 Z= 0.129 Angle : 0.508 5.977 6070 Z= 0.260 Chirality : 0.043 0.232 725 Planarity : 0.005 0.062 782 Dihedral : 9.151 73.932 675 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.36), residues: 564 helix: 1.77 (0.30), residues: 301 sheet: -1.54 (0.52), residues: 88 loop : -0.04 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 470 TYR 0.007 0.001 TYR A 86 PHE 0.015 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.000 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4449) covalent geometry : angle 0.50776 ( 6070) hydrogen bonds : bond 0.02891 ( 231) hydrogen bonds : angle 3.66604 ( 669) Misc. bond : bond 0.00014 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.172 Fit side-chains REVERT: A 38 LYS cc_start: 0.8102 (mppt) cc_final: 0.7327 (mmtt) REVERT: A 39 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7428 (mtm110) REVERT: A 62 ARG cc_start: 0.7397 (ptt90) cc_final: 0.6882 (ptt-90) REVERT: A 88 GLU cc_start: 0.7624 (tp30) cc_final: 0.6993 (mp0) REVERT: A 90 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7808 (mm) REVERT: A 325 ASP cc_start: 0.7775 (t70) cc_final: 0.7360 (t0) REVERT: A 425 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 472 MET cc_start: 0.7621 (mpp) cc_final: 0.7054 (mmt) REVERT: A 492 THR cc_start: 0.8821 (t) cc_final: 0.8571 (m) REVERT: A 510 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7630 (ttpp) REVERT: A 548 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6189 (mt-10) REVERT: A 571 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6737 (pm20) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.5476 time to fit residues: 29.9305 Evaluate side-chains 53 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 548 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129214 restraints weight = 3961.050| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.81 r_work: 0.3124 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4450 Z= 0.122 Angle : 0.497 5.630 6070 Z= 0.256 Chirality : 0.042 0.207 725 Planarity : 0.005 0.062 782 Dihedral : 9.063 74.330 675 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.55 % Allowed : 14.35 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.36), residues: 564 helix: 1.80 (0.30), residues: 302 sheet: -1.55 (0.52), residues: 89 loop : 0.01 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 470 TYR 0.008 0.001 TYR A 137 PHE 0.015 0.001 PHE A 432 TRP 0.004 0.001 TRP A 525 HIS 0.002 0.000 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4449) covalent geometry : angle 0.49686 ( 6070) hydrogen bonds : bond 0.02797 ( 231) hydrogen bonds : angle 3.63448 ( 669) Misc. bond : bond 0.00012 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1451.20 seconds wall clock time: 25 minutes 21.94 seconds (1521.94 seconds total)