Starting phenix.real_space_refine on Wed Mar 4 07:31:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pyc_72030/03_2026/9pyc_72030_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pyc_72030/03_2026/9pyc_72030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pyc_72030/03_2026/9pyc_72030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pyc_72030/03_2026/9pyc_72030.map" model { file = "/net/cci-nas-00/data/ceres_data/9pyc_72030/03_2026/9pyc_72030_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pyc_72030/03_2026/9pyc_72030_neut.cif" } resolution = 2.9 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= 0.002 sd= 0.067 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: 5 Type Number sf(0) Gaussians S 25 5.16 5 C 3578 2.51 5 N 991 2.21 5 O 1085 1.98 5 H 5700 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11379 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 9834 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 31, 'TRANS': 604} Chain breaks: 1 Chain: "F" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1545 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Time building chain proxies: 1.99, per 1000 atoms: 0.17 Number of scatterers: 11379 At special positions: 0 Unit cell: (147.34, 119.78, 72.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 O 1085 8.00 N 991 7.00 C 3578 6.00 H 5700 1.00 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: 0.78 Conformation dependent library (CDL) restraints added in 343.8 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1350 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 10 sheets defined 35.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.643A pdb=" N GLU A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.680A pdb=" N SER A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.803A pdb=" N GLY A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.551A pdb=" N ARG A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.586A pdb=" N LEU A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 442 removed outlier: 3.702A pdb=" N GLU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 549 through 563 removed outlier: 3.887A pdb=" N ALA A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 691 through 700 Processing helix chain 'F' and resid 13 through 25 Processing helix chain 'F' and resid 26 through 31 removed outlier: 3.717A pdb=" N LYS F 29 " --> pdb=" O LYS F 26 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP F 30 " --> pdb=" O LEU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 114 removed outlier: 6.506A pdb=" N MET A 111 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 142 " --> pdb=" O MET A 111 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR A 113 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 262 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 305 through 309 removed outlier: 3.963A pdb=" N THR A 305 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 295 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 359 removed outlier: 7.542A pdb=" N ALA A 319 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR A 339 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 321 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG A 337 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A 323 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP A 381 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 362 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'A' and resid 446 through 449 removed outlier: 3.526A pdb=" N ILE A 416 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 491 through 493 removed outlier: 3.819A pdb=" N LYS A 653 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A 655 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY A 644 " --> pdb=" O HIS A 655 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU A 657 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU A 642 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 493 removed outlier: 5.509A pdb=" N LYS A 618 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE A 684 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU A 620 " --> pdb=" O MET A 682 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N MET A 682 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU A 622 " --> pdb=" O TYR A 680 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR A 680 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 509 removed outlier: 4.919A pdb=" N THR A 499 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET A 522 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 580 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP A 521 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU A 578 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU A 535 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 578 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 537 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N PHE A 580 " --> pdb=" O ILE A 537 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.617A pdb=" N ASN F 4 " --> pdb=" O PRO F 37 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASN F 36 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN F 55 " --> pdb=" O ASN F 36 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5697 1.03 - 1.23: 3 1.23 - 1.42: 2327 1.42 - 1.62: 3405 1.62 - 1.81: 47 Bond restraints: 11479 Sorted by residual: bond pdb=" CA PRO A 166 " pdb=" C PRO A 166 " ideal model delta sigma weight residual 1.527 1.521 0.006 1.07e-02 8.73e+03 3.67e-01 bond pdb=" N PRO A 166 " pdb=" CA PRO A 166 " ideal model delta sigma weight residual 1.479 1.469 0.010 1.71e-02 3.42e+03 3.57e-01 bond pdb=" CA THR A 650 " pdb=" C THR A 650 " ideal model delta sigma weight residual 1.530 1.524 0.006 1.14e-02 7.69e+03 2.85e-01 bond pdb=" CA ILE A 207 " pdb=" CB ILE A 207 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.73e-01 bond pdb=" CA THR A 650 " pdb=" CB THR A 650 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.30e-02 5.92e+03 2.71e-01 ... (remaining 11474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 18873 0.81 - 1.62: 1800 1.62 - 2.43: 122 2.43 - 3.23: 26 3.23 - 4.04: 12 Bond angle restraints: 20833 Sorted by residual: angle pdb=" CA PRO A 166 " pdb=" C PRO A 166 " pdb=" O PRO A 166 " ideal model delta sigma weight residual 123.16 120.52 2.64 1.49e+00 4.50e-01 3.15e+00 angle pdb=" N ALA A 311 " pdb=" CA ALA A 311 " pdb=" C ALA A 311 " ideal model delta sigma weight residual 108.17 111.13 -2.96 1.85e+00 2.92e-01 2.56e+00 angle pdb=" N GLY A 503 " pdb=" CA GLY A 503 " pdb=" C GLY A 503 " ideal model delta sigma weight residual 113.18 109.65 3.53 2.37e+00 1.78e-01 2.22e+00 angle pdb=" N GLY A 199 " pdb=" CA GLY A 199 " pdb=" C GLY A 199 " ideal model delta sigma weight residual 113.18 116.56 -3.38 2.37e+00 1.78e-01 2.04e+00 angle pdb=" C THR A 650 " pdb=" CA THR A 650 " pdb=" CB THR A 650 " ideal model delta sigma weight residual 111.88 109.88 2.00 1.41e+00 5.03e-01 2.01e+00 ... (remaining 20828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 4939 15.01 - 30.02: 276 30.02 - 45.03: 93 45.03 - 60.04: 45 60.04 - 75.05: 3 Dihedral angle restraints: 5356 sinusoidal: 2989 harmonic: 2367 Sorted by residual: dihedral pdb=" CB ARG A 495 " pdb=" CG ARG A 495 " pdb=" CD ARG A 495 " pdb=" NE ARG A 495 " ideal model delta sinusoidal sigma weight residual 180.00 134.74 45.26 3 1.50e+01 4.44e-03 8.14e+00 dihedral pdb=" CB GLU F 28 " pdb=" CG GLU F 28 " pdb=" CD GLU F 28 " pdb=" OE1 GLU F 28 " ideal model delta sinusoidal sigma weight residual 0.00 -75.05 75.05 1 3.00e+01 1.11e-03 7.92e+00 dihedral pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " pdb=" CD1 LEU A 222 " ideal model delta sinusoidal sigma weight residual 180.00 136.27 43.73 3 1.50e+01 4.44e-03 7.86e+00 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 565 0.030 - 0.059: 192 0.059 - 0.089: 53 0.089 - 0.118: 50 0.118 - 0.148: 17 Chirality restraints: 877 Sorted by residual: chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE A 405 " pdb=" N ILE A 405 " pdb=" C ILE A 405 " pdb=" CB ILE A 405 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE A 173 " pdb=" N ILE A 173 " pdb=" C ILE A 173 " pdb=" CB ILE A 173 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 874 not shown) Planarity restraints: 1721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 135 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 136 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 442 " -0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO A 443 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 443 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 443 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 207 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 208 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.016 5.00e-02 4.00e+02 ... (remaining 1718 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.44: 6264 2.44 - 2.98: 26832 2.98 - 3.52: 28683 3.52 - 4.06: 39275 4.06 - 4.60: 57060 Nonbonded interactions: 158114 Sorted by model distance: nonbonded pdb=" HG1 THR A 396 " pdb=" H LEU A 406 " model vdw 1.897 2.100 nonbonded pdb=" H ASN A 369 " pdb=" H LYS A 370 " model vdw 1.953 2.100 nonbonded pdb=" HD3 ARG A 3 " pdb="HH11 ARG A 3 " model vdw 1.992 2.270 nonbonded pdb=" HD2 ARG A 408 " pdb="HH12 ARG A 408 " model vdw 1.993 2.270 nonbonded pdb=" HA TYR A 10 " pdb=" HD1 TYR A 10 " model vdw 2.006 2.270 ... (remaining 158109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.290 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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 : 0.001 0.015 5779 Z= 0.067 Angle : 0.404 4.042 7813 Z= 0.218 Chirality : 0.042 0.148 877 Planarity : 0.004 0.030 1028 Dihedral : 9.759 75.052 2186 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.00 (0.32), residues: 726 helix: 1.66 (0.35), residues: 232 sheet: -1.04 (0.36), residues: 207 loop : -0.44 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.004 0.001 TYR A 10 PHE 0.004 0.001 PHE A 411 TRP 0.003 0.000 TRP A 448 HIS 0.001 0.000 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00143 ( 5779) covalent geometry : angle 0.40399 ( 7813) hydrogen bonds : bond 0.24745 ( 259) hydrogen bonds : angle 8.65346 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 HIS cc_start: 0.7382 (m-70) cc_final: 0.7035 (m90) REVERT: A 211 MET cc_start: 0.4385 (mtm) cc_final: 0.3830 (mpp) REVERT: A 420 VAL cc_start: 0.7296 (m) cc_final: 0.6903 (m) REVERT: A 508 GLN cc_start: 0.7773 (tt0) cc_final: 0.7476 (tm-30) REVERT: A 675 LYS cc_start: 0.8397 (mttt) cc_final: 0.8015 (tmtt) REVERT: F 43 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8640 (ttpm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 1.5233 time to fit residues: 184.2870 Evaluate side-chains 62 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.100523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.084016 restraints weight = 69147.143| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.49 r_work: 0.3854 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5779 Z= 0.128 Angle : 0.499 5.471 7813 Z= 0.265 Chirality : 0.043 0.139 877 Planarity : 0.005 0.058 1028 Dihedral : 2.272 8.609 786 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.50 % Allowed : 9.75 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.32), residues: 726 helix: 1.69 (0.33), residues: 236 sheet: -0.89 (0.37), residues: 207 loop : -0.37 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.006 0.001 TYR A 666 PHE 0.018 0.001 PHE A 151 TRP 0.004 0.001 TRP A 448 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5779) covalent geometry : angle 0.49885 ( 7813) hydrogen bonds : bond 0.06679 ( 259) hydrogen bonds : angle 6.67793 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6902 (mt0) REVERT: A 508 GLN cc_start: 0.7827 (tt0) cc_final: 0.7438 (tm130) REVERT: A 675 LYS cc_start: 0.8579 (mttt) cc_final: 0.8088 (tmtt) outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 1.3562 time to fit residues: 91.6106 Evaluate side-chains 52 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 630 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.098180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.080907 restraints weight = 69966.139| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.57 r_work: 0.3788 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5779 Z= 0.203 Angle : 0.541 4.599 7813 Z= 0.288 Chirality : 0.043 0.143 877 Planarity : 0.005 0.047 1028 Dihedral : 3.027 12.919 786 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.16 % Allowed : 10.25 % Favored : 88.60 % 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: 0.05 (0.32), residues: 726 helix: 1.65 (0.33), residues: 232 sheet: -0.95 (0.36), residues: 212 loop : -0.37 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.008 0.001 TYR A 666 PHE 0.011 0.001 PHE A 140 TRP 0.005 0.002 TRP A 127 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 5779) covalent geometry : angle 0.54130 ( 7813) hydrogen bonds : bond 0.04753 ( 259) hydrogen bonds : angle 6.19758 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 LYS cc_start: 0.8565 (mttt) cc_final: 0.8093 (tmtt) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 1.1289 time to fit residues: 61.6084 Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.096129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.078946 restraints weight = 70158.490| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.51 r_work: 0.3735 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5779 Z= 0.264 Angle : 0.603 8.426 7813 Z= 0.322 Chirality : 0.044 0.141 877 Planarity : 0.005 0.048 1028 Dihedral : 3.921 14.882 786 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.82 % Allowed : 11.57 % Favored : 86.61 % 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: -0.48 (0.31), residues: 726 helix: 0.99 (0.33), residues: 232 sheet: -1.09 (0.36), residues: 207 loop : -0.64 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 437 TYR 0.012 0.002 TYR A 204 PHE 0.012 0.002 PHE A 140 TRP 0.008 0.002 TRP A 127 HIS 0.008 0.002 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 5779) covalent geometry : angle 0.60350 ( 7813) hydrogen bonds : bond 0.04503 ( 259) hydrogen bonds : angle 6.13078 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7326 (mt0) REVERT: A 410 GLU cc_start: 0.6553 (mp0) cc_final: 0.4742 (tp30) REVERT: A 451 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8115 (tp30) REVERT: A 675 LYS cc_start: 0.8559 (mttt) cc_final: 0.8032 (tmtt) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 1.2853 time to fit residues: 75.4081 Evaluate side-chains 47 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 700 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 13 optimal weight: 0.0670 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 overall best weight: 4.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.096529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.079553 restraints weight = 69799.406| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.50 r_work: 0.3750 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5779 Z= 0.147 Angle : 0.514 6.154 7813 Z= 0.270 Chirality : 0.043 0.133 877 Planarity : 0.005 0.082 1028 Dihedral : 3.664 13.015 786 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.16 % Allowed : 12.73 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.20 (0.31), residues: 726 helix: 1.32 (0.34), residues: 232 sheet: -0.92 (0.37), residues: 201 loop : -0.59 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.007 0.001 TYR A 204 PHE 0.007 0.001 PHE A 684 TRP 0.004 0.001 TRP A 127 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5779) covalent geometry : angle 0.51426 ( 7813) hydrogen bonds : bond 0.04016 ( 259) hydrogen bonds : angle 5.72621 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: A 410 GLU cc_start: 0.6443 (mp0) cc_final: 0.4757 (tp30) REVERT: A 675 LYS cc_start: 0.8572 (mttt) cc_final: 0.8001 (tmtt) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 1.1856 time to fit residues: 64.6488 Evaluate side-chains 46 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.096531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.079812 restraints weight = 70495.808| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.50 r_work: 0.3755 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5779 Z= 0.136 Angle : 0.511 5.816 7813 Z= 0.267 Chirality : 0.043 0.135 877 Planarity : 0.004 0.061 1028 Dihedral : 3.602 12.140 786 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.99 % Allowed : 13.88 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.03 (0.31), residues: 726 helix: 1.51 (0.33), residues: 232 sheet: -0.88 (0.36), residues: 202 loop : -0.50 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.006 0.001 TYR A 204 PHE 0.006 0.001 PHE A 593 TRP 0.005 0.001 TRP A 127 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5779) covalent geometry : angle 0.51074 ( 7813) hydrogen bonds : bond 0.03799 ( 259) hydrogen bonds : angle 5.55357 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7084 (mt0) REVERT: A 410 GLU cc_start: 0.6504 (mp0) cc_final: 0.4846 (tp30) REVERT: A 675 LYS cc_start: 0.8572 (mttt) cc_final: 0.7987 (tmtt) REVERT: A 682 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7760 (ttp) REVERT: F 95 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6345 (mmp-170) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 1.1681 time to fit residues: 62.8812 Evaluate side-chains 50 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain F residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.096798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.080246 restraints weight = 70267.602| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.50 r_work: 0.3759 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5779 Z= 0.109 Angle : 0.490 6.157 7813 Z= 0.254 Chirality : 0.043 0.136 877 Planarity : 0.004 0.052 1028 Dihedral : 3.491 11.142 786 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.50 % Allowed : 14.55 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.32), residues: 726 helix: 1.74 (0.34), residues: 232 sheet: -0.91 (0.36), residues: 209 loop : -0.32 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.005 0.001 TYR A 204 PHE 0.026 0.001 PHE A 151 TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5779) covalent geometry : angle 0.48961 ( 7813) hydrogen bonds : bond 0.03594 ( 259) hydrogen bonds : angle 5.37690 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: A 410 GLU cc_start: 0.6479 (mp0) cc_final: 0.4867 (tp30) REVERT: A 435 LEU cc_start: 0.8779 (mp) cc_final: 0.8557 (tp) REVERT: A 675 LYS cc_start: 0.8589 (mttt) cc_final: 0.7998 (tmtt) REVERT: F 95 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6577 (mmp-170) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 1.2131 time to fit residues: 61.3208 Evaluate side-chains 47 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain F residue 95 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 0.0870 chunk 8 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.097193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.080566 restraints weight = 70123.524| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.52 r_work: 0.3767 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5779 Z= 0.111 Angle : 0.487 6.341 7813 Z= 0.254 Chirality : 0.043 0.135 877 Planarity : 0.004 0.048 1028 Dihedral : 3.464 11.613 786 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.99 % Allowed : 13.72 % Favored : 85.29 % 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: 0.26 (0.32), residues: 726 helix: 1.79 (0.34), residues: 233 sheet: -0.87 (0.36), residues: 209 loop : -0.22 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.004 0.001 TYR A 204 PHE 0.017 0.001 PHE A 151 TRP 0.004 0.001 TRP A 127 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5779) covalent geometry : angle 0.48716 ( 7813) hydrogen bonds : bond 0.03499 ( 259) hydrogen bonds : angle 5.27376 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7041 (mt0) REVERT: A 410 GLU cc_start: 0.6420 (mp0) cc_final: 0.4818 (tp30) REVERT: A 435 LEU cc_start: 0.8781 (mp) cc_final: 0.8573 (tp) REVERT: A 675 LYS cc_start: 0.8603 (mttt) cc_final: 0.7999 (tmtt) REVERT: A 682 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7628 (ttp) REVERT: F 46 GLN cc_start: 0.5790 (mp10) cc_final: 0.5549 (mp10) REVERT: F 95 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6556 (mmp-170) outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 1.1191 time to fit residues: 55.5601 Evaluate side-chains 48 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain F residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.095992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.079327 restraints weight = 69595.917| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.50 r_work: 0.3749 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5779 Z= 0.165 Angle : 0.512 6.042 7813 Z= 0.270 Chirality : 0.043 0.135 877 Planarity : 0.004 0.053 1028 Dihedral : 3.655 12.768 786 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.83 % Allowed : 14.05 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.32), residues: 726 helix: 1.62 (0.33), residues: 233 sheet: -0.89 (0.36), residues: 211 loop : -0.28 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 437 TYR 0.008 0.001 TYR A 204 PHE 0.015 0.001 PHE A 151 TRP 0.005 0.001 TRP F 30 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 5779) covalent geometry : angle 0.51175 ( 7813) hydrogen bonds : bond 0.03667 ( 259) hydrogen bonds : angle 5.37481 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7251 (mt0) REVERT: A 410 GLU cc_start: 0.6504 (mp0) cc_final: 0.4863 (tp30) REVERT: A 675 LYS cc_start: 0.8580 (mttt) cc_final: 0.7987 (tmtt) outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 1.1465 time to fit residues: 55.6214 Evaluate side-chains 45 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.096704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.080064 restraints weight = 70065.894| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.55 r_work: 0.3768 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5779 Z= 0.107 Angle : 0.490 7.356 7813 Z= 0.255 Chirality : 0.043 0.137 877 Planarity : 0.004 0.046 1028 Dihedral : 3.513 12.169 786 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.33 % Allowed : 14.71 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.32), residues: 726 helix: 1.90 (0.34), residues: 233 sheet: -0.70 (0.36), residues: 204 loop : -0.24 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 437 TYR 0.005 0.001 TYR A 204 PHE 0.016 0.001 PHE A 151 TRP 0.004 0.001 TRP A 127 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5779) covalent geometry : angle 0.49024 ( 7813) hydrogen bonds : bond 0.03405 ( 259) hydrogen bonds : angle 5.18239 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7199 (mt0) REVERT: A 410 GLU cc_start: 0.6484 (mp0) cc_final: 0.4833 (tp30) REVERT: A 675 LYS cc_start: 0.8598 (mttt) cc_final: 0.7984 (tmtt) REVERT: F 46 GLN cc_start: 0.6166 (mp10) cc_final: 0.5867 (mp10) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 1.1805 time to fit residues: 55.9693 Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 630 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 58 optimal weight: 0.0270 chunk 5 optimal weight: 40.0000 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 3.9844 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.096461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.079850 restraints weight = 70472.100| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.52 r_work: 0.3750 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5779 Z= 0.139 Angle : 0.499 7.367 7813 Z= 0.261 Chirality : 0.042 0.133 877 Planarity : 0.004 0.045 1028 Dihedral : 3.553 12.404 786 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.83 % Allowed : 14.21 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.35 (0.32), residues: 726 helix: 1.92 (0.34), residues: 233 sheet: -0.85 (0.36), residues: 211 loop : -0.19 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 437 TYR 0.007 0.001 TYR A 204 PHE 0.014 0.001 PHE A 151 TRP 0.004 0.001 TRP F 30 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5779) covalent geometry : angle 0.49932 ( 7813) hydrogen bonds : bond 0.03459 ( 259) hydrogen bonds : angle 5.20948 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5255.69 seconds wall clock time: 89 minutes 20.48 seconds (5360.48 seconds total)