Starting phenix.real_space_refine on Wed Feb 4 10:23:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxo_61870/02_2026/9jxo_61870.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxo_61870/02_2026/9jxo_61870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxo_61870/02_2026/9jxo_61870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxo_61870/02_2026/9jxo_61870.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxo_61870/02_2026/9jxo_61870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxo_61870/02_2026/9jxo_61870.cif" } resolution = 3.48 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6544 2.51 5 N 1630 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s 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: 9906 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4953 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 575} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 3.14, per 1000 atoms: 0.32 Number of scatterers: 9906 At special positions: 0 Unit cell: (127.655, 106.555, 102.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1692 8.00 N 1630 7.00 C 6544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 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: 0.80 Conformation dependent library (CDL) restraints added in 401.4 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 76.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 44 through 101 Processing helix chain 'A' and resid 125 through 168 removed outlier: 3.511A pdb=" N HIS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.703A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.703A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.730A pdb=" N GLN A 227 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 258 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 272 through 296 removed outlier: 3.717A pdb=" N LEU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.886A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.958A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.738A pdb=" N ALA A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 447 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 479 through 503 removed outlier: 3.638A pdb=" N TYR A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 533 removed outlier: 4.139A pdb=" N THR A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.101A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 590 through 596 Processing helix chain 'A' and resid 600 through 618 removed outlier: 3.851A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 44 through 101 Processing helix chain 'B' and resid 125 through 168 removed outlier: 3.511A pdb=" N HIS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 180 removed outlier: 3.704A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 206 Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.703A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.730A pdb=" N GLN B 227 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 258 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 272 through 296 removed outlier: 3.718A pdb=" N LEU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.887A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.957A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 391 through 400 removed outlier: 3.738A pdb=" N ALA B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 447 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 479 through 503 removed outlier: 3.637A pdb=" N TYR B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR B 485 " --> pdb=" O GLY B 481 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 533 removed outlier: 4.139A pdb=" N THR B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 4.102A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 581 Processing helix chain 'B' and resid 590 through 596 Processing helix chain 'B' and resid 600 through 618 removed outlier: 3.850A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1516 1.31 - 1.44: 3076 1.44 - 1.56: 5544 1.56 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10192 Sorted by residual: bond pdb=" C LEU B 282 " pdb=" O LEU B 282 " ideal model delta sigma weight residual 1.236 1.191 0.046 1.33e-02 5.65e+03 1.18e+01 bond pdb=" C LEU A 282 " pdb=" O LEU A 282 " ideal model delta sigma weight residual 1.236 1.191 0.046 1.33e-02 5.65e+03 1.17e+01 bond pdb=" C LEU B 284 " pdb=" O LEU B 284 " ideal model delta sigma weight residual 1.236 1.195 0.042 1.28e-02 6.10e+03 1.06e+01 bond pdb=" C LEU A 284 " pdb=" O LEU A 284 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.28e-02 6.10e+03 1.02e+01 bond pdb=" N ILE B 629 " pdb=" CA ILE B 629 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.22e-02 6.72e+03 8.90e+00 ... (remaining 10187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 13660 3.23 - 6.46: 130 6.46 - 9.70: 18 9.70 - 12.93: 2 12.93 - 16.16: 6 Bond angle restraints: 13816 Sorted by residual: angle pdb=" N ASP A 628 " pdb=" CA ASP A 628 " pdb=" C ASP A 628 " ideal model delta sigma weight residual 110.24 94.08 16.16 1.47e+00 4.63e-01 1.21e+02 angle pdb=" N ASP B 628 " pdb=" CA ASP B 628 " pdb=" C ASP B 628 " ideal model delta sigma weight residual 110.24 94.10 16.14 1.47e+00 4.63e-01 1.21e+02 angle pdb=" C ASP A 628 " pdb=" CA ASP A 628 " pdb=" CB ASP A 628 " ideal model delta sigma weight residual 109.84 124.82 -14.98 1.50e+00 4.44e-01 9.97e+01 angle pdb=" C ASP B 628 " pdb=" CA ASP B 628 " pdb=" CB ASP B 628 " ideal model delta sigma weight residual 109.84 124.74 -14.90 1.50e+00 4.44e-01 9.87e+01 angle pdb=" N ILE B 629 " pdb=" CA ILE B 629 " pdb=" C ILE B 629 " ideal model delta sigma weight residual 108.89 94.20 14.69 1.52e+00 4.33e-01 9.34e+01 ... (remaining 13811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5188 17.96 - 35.92: 570 35.92 - 53.89: 150 53.89 - 71.85: 18 71.85 - 89.81: 10 Dihedral angle restraints: 5936 sinusoidal: 2398 harmonic: 3538 Sorted by residual: dihedral pdb=" CA ARG B 570 " pdb=" C ARG B 570 " pdb=" N PHE B 571 " pdb=" CA PHE B 571 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ARG A 570 " pdb=" C ARG A 570 " pdb=" N PHE A 571 " pdb=" CA PHE A 571 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA PHE B 394 " pdb=" C PHE B 394 " pdb=" N TRP B 395 " pdb=" CA TRP B 395 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1317 0.074 - 0.149: 171 0.149 - 0.223: 14 0.223 - 0.297: 2 0.297 - 0.372: 2 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CA ILE B 629 " pdb=" N ILE B 629 " pdb=" C ILE B 629 " pdb=" CB ILE B 629 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA ILE A 629 " pdb=" N ILE A 629 " pdb=" C ILE A 629 " pdb=" CB ILE A 629 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA PHE A 283 " pdb=" N PHE A 283 " pdb=" C PHE A 283 " pdb=" CB PHE A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1503 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 617 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C LEU A 617 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU A 617 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN A 618 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 231 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ALA B 231 " 0.060 2.00e-02 2.50e+03 pdb=" O ALA B 231 " -0.022 2.00e-02 2.50e+03 pdb=" N TRP B 232 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 231 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ALA A 231 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA A 231 " 0.022 2.00e-02 2.50e+03 pdb=" N TRP A 232 " 0.020 2.00e-02 2.50e+03 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 14 2.20 - 2.88: 3992 2.88 - 3.55: 14936 3.55 - 4.23: 22164 4.23 - 4.90: 38672 Nonbonded interactions: 79778 Sorted by model distance: nonbonded pdb=" CE1 TYR B 368 " pdb=" CE2 PHE B 372 " model vdw 1.526 3.640 nonbonded pdb=" CE1 TYR A 368 " pdb=" CE2 PHE A 372 " model vdw 1.526 3.640 nonbonded pdb=" CD1 TYR B 368 " pdb=" CE2 PHE B 372 " model vdw 1.579 3.640 nonbonded pdb=" CD1 TYR A 368 " pdb=" CE2 PHE A 372 " model vdw 1.580 3.640 nonbonded pdb=" CE1 TYR A 368 " pdb=" CD2 PHE A 372 " model vdw 1.911 3.640 ... (remaining 79773 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.130 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.010 0.073 10194 Z= 0.425 Angle : 0.922 16.159 13820 Z= 0.558 Chirality : 0.053 0.372 1506 Planarity : 0.005 0.038 1714 Dihedral : 16.135 89.811 3634 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.38 % Allowed : 17.71 % Favored : 81.91 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.00 % 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: -2.05 (0.23), residues: 1176 helix: -0.68 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -3.19 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 171 TYR 0.018 0.002 TYR A 553 PHE 0.037 0.002 PHE B 394 TRP 0.024 0.002 TRP A 607 HIS 0.009 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00960 (10192) covalent geometry : angle 0.92163 (13816) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.42661 ( 4) hydrogen bonds : bond 0.08801 ( 664) hydrogen bonds : angle 4.01911 ( 1968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.8442 (t70) cc_final: 0.8218 (t70) REVERT: A 213 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7761 (mtmm) REVERT: A 219 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7362 (ttm-80) REVERT: A 283 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6548 (t80) REVERT: A 425 GLU cc_start: 0.8307 (pt0) cc_final: 0.8099 (pt0) REVERT: A 532 MET cc_start: 0.7534 (mtp) cc_final: 0.7318 (mtp) REVERT: B 213 LYS cc_start: 0.8440 (mtmt) cc_final: 0.7930 (mtmm) REVERT: B 215 MET cc_start: 0.8239 (mmm) cc_final: 0.8018 (mmm) REVERT: B 283 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6476 (t80) REVERT: B 425 GLU cc_start: 0.8287 (pt0) cc_final: 0.8084 (pt0) REVERT: B 532 MET cc_start: 0.7557 (mtp) cc_final: 0.7354 (mtp) outliers start: 4 outliers final: 0 residues processed: 182 average time/residue: 0.0901 time to fit residues: 22.9464 Evaluate side-chains 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain B residue 283 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 193 GLN A 288 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 193 GLN B 288 ASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125074 restraints weight = 12244.033| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.06 r_work: 0.3076 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10194 Z= 0.142 Angle : 0.561 10.159 13820 Z= 0.297 Chirality : 0.040 0.150 1506 Planarity : 0.004 0.044 1714 Dihedral : 5.082 53.860 1310 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.46 % Allowed : 20.08 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.25 (0.25), residues: 1176 helix: 0.74 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -2.74 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 171 TYR 0.013 0.001 TYR A 186 PHE 0.028 0.002 PHE B 372 TRP 0.017 0.001 TRP B 607 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00325 (10192) covalent geometry : angle 0.56084 (13816) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.66939 ( 4) hydrogen bonds : bond 0.03933 ( 664) hydrogen bonds : angle 4.10303 ( 1968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7662 (mtp-110) REVERT: A 210 ASP cc_start: 0.8430 (t70) cc_final: 0.8039 (t70) REVERT: A 213 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7644 (mtmm) REVERT: A 219 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7197 (ttm-80) REVERT: A 283 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6834 (t80) REVERT: A 335 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7095 (m-10) REVERT: A 425 GLU cc_start: 0.8317 (pt0) cc_final: 0.8028 (pt0) REVERT: A 532 MET cc_start: 0.8355 (mtp) cc_final: 0.8022 (mtp) REVERT: B 23 GLU cc_start: 0.7631 (tp30) cc_final: 0.7287 (tp30) REVERT: B 210 ASP cc_start: 0.8465 (t70) cc_final: 0.8096 (t0) REVERT: B 213 LYS cc_start: 0.8445 (mtmt) cc_final: 0.7788 (mtmm) REVERT: B 283 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6863 (t80) REVERT: B 335 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: B 425 GLU cc_start: 0.8342 (pt0) cc_final: 0.8086 (pt0) REVERT: B 532 MET cc_start: 0.8381 (mtp) cc_final: 0.8063 (mtp) outliers start: 26 outliers final: 7 residues processed: 174 average time/residue: 0.0917 time to fit residues: 22.1242 Evaluate side-chains 155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 0.0050 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.174600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127496 restraints weight = 12182.635| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.16 r_work: 0.3100 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10194 Z= 0.115 Angle : 0.499 6.925 13820 Z= 0.267 Chirality : 0.038 0.148 1506 Planarity : 0.004 0.034 1714 Dihedral : 4.760 50.948 1310 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.46 % Allowed : 21.50 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.44 (0.25), residues: 1176 helix: 1.27 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.71 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.014 0.001 TYR A 496 PHE 0.019 0.001 PHE A 372 TRP 0.015 0.001 TRP B 607 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00255 (10192) covalent geometry : angle 0.49937 (13816) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.61255 ( 4) hydrogen bonds : bond 0.03519 ( 664) hydrogen bonds : angle 3.99025 ( 1968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.8499 (t0) cc_final: 0.8140 (t0) REVERT: A 210 ASP cc_start: 0.8502 (t70) cc_final: 0.8144 (t0) REVERT: A 213 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7532 (mtmm) REVERT: A 215 MET cc_start: 0.8213 (mmm) cc_final: 0.7987 (mmm) REVERT: A 219 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7189 (ttm-80) REVERT: A 283 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6742 (t80) REVERT: A 335 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: A 532 MET cc_start: 0.8280 (mtp) cc_final: 0.7949 (mtp) REVERT: B 92 GLN cc_start: 0.9105 (tp40) cc_final: 0.8710 (mm110) REVERT: B 152 ASN cc_start: 0.8446 (t0) cc_final: 0.8034 (t0) REVERT: B 181 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: B 210 ASP cc_start: 0.8474 (t70) cc_final: 0.8074 (t0) REVERT: B 213 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7707 (mtmm) REVERT: B 283 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6684 (t80) REVERT: B 335 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: B 425 GLU cc_start: 0.8295 (pt0) cc_final: 0.8064 (pt0) REVERT: B 532 MET cc_start: 0.8318 (mtp) cc_final: 0.8008 (mtp) outliers start: 26 outliers final: 9 residues processed: 173 average time/residue: 0.0777 time to fit residues: 19.4716 Evaluate side-chains 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.173976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112996 restraints weight = 12561.466| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.72 r_work: 0.3115 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10194 Z= 0.124 Angle : 0.520 9.379 13820 Z= 0.271 Chirality : 0.039 0.155 1506 Planarity : 0.004 0.044 1714 Dihedral : 4.622 49.002 1310 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.56 % Allowed : 24.15 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.69 (0.25), residues: 1176 helix: 1.46 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.67 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.011 0.001 TYR B 496 PHE 0.016 0.001 PHE A 357 TRP 0.013 0.001 TRP B 607 HIS 0.003 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00287 (10192) covalent geometry : angle 0.52005 (13816) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.53173 ( 4) hydrogen bonds : bond 0.03440 ( 664) hydrogen bonds : angle 3.93298 ( 1968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.8434 (t70) cc_final: 0.8175 (t0) REVERT: A 213 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7624 (mtpt) REVERT: A 215 MET cc_start: 0.7890 (mmm) cc_final: 0.7628 (mmm) REVERT: A 219 ARG cc_start: 0.7052 (ttm-80) cc_final: 0.6732 (ttm-80) REVERT: A 335 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: A 532 MET cc_start: 0.8130 (mtp) cc_final: 0.7728 (mtp) REVERT: B 92 GLN cc_start: 0.9249 (tp40) cc_final: 0.8909 (mm110) REVERT: B 181 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: B 210 ASP cc_start: 0.8387 (t70) cc_final: 0.8082 (t0) REVERT: B 213 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7816 (mtpt) REVERT: B 335 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6822 (m-10) REVERT: B 425 GLU cc_start: 0.8332 (pt0) cc_final: 0.8091 (pt0) REVERT: B 532 MET cc_start: 0.8110 (mtp) cc_final: 0.7742 (mtt) outliers start: 27 outliers final: 11 residues processed: 164 average time/residue: 0.0841 time to fit residues: 19.8220 Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 0.0470 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111710 restraints weight = 12502.676| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.69 r_work: 0.3098 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10194 Z= 0.143 Angle : 0.530 7.666 13820 Z= 0.277 Chirality : 0.040 0.156 1506 Planarity : 0.004 0.046 1714 Dihedral : 4.128 20.792 1306 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.65 % Allowed : 24.53 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.87 (0.25), residues: 1176 helix: 1.55 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -2.49 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 472 TYR 0.015 0.001 TYR B 518 PHE 0.019 0.001 PHE B 394 TRP 0.013 0.001 TRP B 607 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00337 (10192) covalent geometry : angle 0.52988 (13816) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.47361 ( 4) hydrogen bonds : bond 0.03482 ( 664) hydrogen bonds : angle 3.93159 ( 1968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7489 (tp30) cc_final: 0.7234 (tm-30) REVERT: A 210 ASP cc_start: 0.8398 (t70) cc_final: 0.8072 (t70) REVERT: A 213 LYS cc_start: 0.8031 (mtmt) cc_final: 0.7617 (mtpt) REVERT: A 215 MET cc_start: 0.7881 (mmm) cc_final: 0.7596 (mmm) REVERT: A 219 ARG cc_start: 0.7062 (ttm-80) cc_final: 0.6700 (ttm-80) REVERT: A 335 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6787 (m-10) REVERT: A 532 MET cc_start: 0.8085 (mtp) cc_final: 0.7693 (mtp) REVERT: B 181 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 210 ASP cc_start: 0.8423 (t70) cc_final: 0.8097 (t0) REVERT: B 213 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7753 (mtpt) REVERT: B 335 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6814 (m-10) REVERT: B 532 MET cc_start: 0.8083 (mtp) cc_final: 0.7678 (mtp) outliers start: 28 outliers final: 15 residues processed: 168 average time/residue: 0.0947 time to fit residues: 21.9277 Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.171334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110881 restraints weight = 12521.969| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.66 r_work: 0.3090 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10194 Z= 0.153 Angle : 0.537 7.185 13820 Z= 0.278 Chirality : 0.040 0.163 1506 Planarity : 0.004 0.044 1714 Dihedral : 4.132 21.088 1306 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.50 % Allowed : 23.77 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.25), residues: 1176 helix: 1.57 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -2.34 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 472 TYR 0.015 0.001 TYR A 496 PHE 0.020 0.001 PHE B 394 TRP 0.013 0.001 TRP A 607 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00364 (10192) covalent geometry : angle 0.53677 (13816) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.44933 ( 4) hydrogen bonds : bond 0.03495 ( 664) hydrogen bonds : angle 3.96441 ( 1968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7574 (tp30) cc_final: 0.7313 (tm-30) REVERT: A 210 ASP cc_start: 0.8386 (t70) cc_final: 0.8058 (t70) REVERT: A 213 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7613 (mtpt) REVERT: A 215 MET cc_start: 0.7880 (mmm) cc_final: 0.7574 (mmm) REVERT: A 219 ARG cc_start: 0.7050 (ttm-80) cc_final: 0.6679 (ttm-80) REVERT: A 335 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6827 (m-10) REVERT: A 532 MET cc_start: 0.8080 (mtp) cc_final: 0.7699 (mtp) REVERT: A 549 GLU cc_start: 0.8903 (tt0) cc_final: 0.8288 (tp30) REVERT: B 210 ASP cc_start: 0.8432 (t70) cc_final: 0.8200 (t0) REVERT: B 335 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: B 532 MET cc_start: 0.8094 (mtp) cc_final: 0.7691 (mtp) REVERT: B 549 GLU cc_start: 0.8910 (tt0) cc_final: 0.8410 (tp30) outliers start: 37 outliers final: 21 residues processed: 180 average time/residue: 0.0925 time to fit residues: 23.5081 Evaluate side-chains 171 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 35 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111466 restraints weight = 12418.538| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.66 r_work: 0.3094 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10194 Z= 0.139 Angle : 0.541 8.481 13820 Z= 0.280 Chirality : 0.040 0.186 1506 Planarity : 0.004 0.037 1714 Dihedral : 4.090 20.911 1306 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.12 % Allowed : 24.34 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.05 (0.25), residues: 1176 helix: 1.63 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -2.25 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.022 0.001 TYR A 22 PHE 0.018 0.001 PHE B 357 TRP 0.014 0.001 TRP A 607 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00326 (10192) covalent geometry : angle 0.54062 (13816) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.46851 ( 4) hydrogen bonds : bond 0.03459 ( 664) hydrogen bonds : angle 3.96452 ( 1968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7705 (tp30) cc_final: 0.7474 (tm-30) REVERT: A 210 ASP cc_start: 0.8371 (t70) cc_final: 0.8029 (t70) REVERT: A 213 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7626 (mtpt) REVERT: A 215 MET cc_start: 0.7888 (mmm) cc_final: 0.7597 (mmm) REVERT: A 219 ARG cc_start: 0.7033 (ttm-80) cc_final: 0.6663 (ttm-80) REVERT: A 335 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: A 532 MET cc_start: 0.8062 (mtp) cc_final: 0.7662 (mtp) REVERT: A 549 GLU cc_start: 0.8953 (tt0) cc_final: 0.8353 (tp30) REVERT: B 210 ASP cc_start: 0.8469 (t70) cc_final: 0.8165 (t70) REVERT: B 335 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6893 (m-10) REVERT: B 532 MET cc_start: 0.8085 (mtp) cc_final: 0.7709 (mtp) REVERT: B 549 GLU cc_start: 0.8922 (tt0) cc_final: 0.8430 (tp30) outliers start: 33 outliers final: 22 residues processed: 169 average time/residue: 0.0871 time to fit residues: 20.9100 Evaluate side-chains 169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 81 GLN A 88 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 88 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108692 restraints weight = 12655.921| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.70 r_work: 0.3011 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 10194 Z= 0.344 Angle : 0.711 9.828 13820 Z= 0.366 Chirality : 0.048 0.175 1506 Planarity : 0.005 0.053 1714 Dihedral : 4.589 23.457 1306 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.56 % Allowed : 24.72 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.51 (0.25), residues: 1176 helix: 1.23 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.36 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 82 TYR 0.018 0.002 TYR A 553 PHE 0.030 0.002 PHE B 394 TRP 0.014 0.002 TRP A 607 HIS 0.008 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00836 (10192) covalent geometry : angle 0.71085 (13816) SS BOND : bond 0.00076 ( 2) SS BOND : angle 0.33636 ( 4) hydrogen bonds : bond 0.04342 ( 664) hydrogen bonds : angle 4.32982 ( 1968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.9035 (mtm-85) cc_final: 0.8057 (mtm-85) REVERT: A 130 ASP cc_start: 0.8133 (m-30) cc_final: 0.7697 (t70) REVERT: A 210 ASP cc_start: 0.8336 (t70) cc_final: 0.8063 (t70) REVERT: A 219 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6855 (ttm-80) REVERT: A 468 ARG cc_start: 0.6904 (ttm170) cc_final: 0.6586 (ttp-170) REVERT: A 532 MET cc_start: 0.8147 (mtp) cc_final: 0.7767 (mtp) REVERT: A 549 GLU cc_start: 0.8917 (tt0) cc_final: 0.8369 (tp30) REVERT: B 82 ARG cc_start: 0.8954 (mtm-85) cc_final: 0.8056 (mtm-85) REVERT: B 130 ASP cc_start: 0.8091 (m-30) cc_final: 0.7652 (t70) REVERT: B 210 ASP cc_start: 0.8471 (t70) cc_final: 0.8119 (t70) REVERT: B 468 ARG cc_start: 0.6851 (ttm170) cc_final: 0.6535 (ttp-170) REVERT: B 532 MET cc_start: 0.8157 (mtp) cc_final: 0.7764 (mtp) REVERT: B 549 GLU cc_start: 0.8886 (tt0) cc_final: 0.8351 (tp30) outliers start: 27 outliers final: 19 residues processed: 171 average time/residue: 0.0964 time to fit residues: 22.6932 Evaluate side-chains 166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121397 restraints weight = 12371.518| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.23 r_work: 0.2974 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.007 0.052 10194 Z= 0.282 Angle : 0.671 9.510 13820 Z= 0.346 Chirality : 0.046 0.182 1506 Planarity : 0.005 0.051 1714 Dihedral : 4.583 23.767 1306 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.37 % Allowed : 25.47 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.45 (0.25), residues: 1176 helix: 1.17 (0.18), residues: 874 sheet: None (None), residues: 0 loop : -2.31 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 82 TYR 0.017 0.002 TYR A 496 PHE 0.026 0.002 PHE B 394 TRP 0.016 0.002 TRP A 607 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00686 (10192) covalent geometry : angle 0.67057 (13816) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.38517 ( 4) hydrogen bonds : bond 0.04150 ( 664) hydrogen bonds : angle 4.33743 ( 1968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8021 (tp30) cc_final: 0.7646 (tm-30) REVERT: A 28 MET cc_start: 0.8767 (tpp) cc_final: 0.8452 (tpp) REVERT: A 130 ASP cc_start: 0.8205 (m-30) cc_final: 0.7893 (t70) REVERT: A 210 ASP cc_start: 0.8367 (t70) cc_final: 0.8072 (t0) REVERT: A 213 LYS cc_start: 0.8385 (mtmt) cc_final: 0.7864 (mtpt) REVERT: A 215 MET cc_start: 0.8362 (mmm) cc_final: 0.8139 (mmm) REVERT: A 219 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7490 (ttm-80) REVERT: A 532 MET cc_start: 0.8383 (mtp) cc_final: 0.8165 (mtp) REVERT: A 549 GLU cc_start: 0.8823 (tt0) cc_final: 0.8514 (tp30) REVERT: B 82 ARG cc_start: 0.9100 (mtm-85) cc_final: 0.8208 (mtm-85) REVERT: B 130 ASP cc_start: 0.8179 (m-30) cc_final: 0.7847 (t70) REVERT: B 210 ASP cc_start: 0.8359 (t70) cc_final: 0.8056 (t70) REVERT: B 213 LYS cc_start: 0.8448 (mtmt) cc_final: 0.7913 (mtpt) REVERT: B 314 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7796 (mt0) REVERT: B 532 MET cc_start: 0.8319 (mtp) cc_final: 0.8063 (mtp) REVERT: B 549 GLU cc_start: 0.8775 (tt0) cc_final: 0.8474 (tp30) REVERT: B 617 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8343 (mp) outliers start: 25 outliers final: 20 residues processed: 170 average time/residue: 0.0790 time to fit residues: 19.0209 Evaluate side-chains 172 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 79 optimal weight: 0.0010 chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** 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 = 0.3970 r_free = 0.3970 target = 0.172001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112007 restraints weight = 12375.350| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.68 r_work: 0.3106 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10194 Z= 0.124 Angle : 0.558 9.860 13820 Z= 0.291 Chirality : 0.040 0.178 1506 Planarity : 0.004 0.033 1714 Dihedral : 4.221 21.958 1306 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.99 % Allowed : 26.04 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.99 (0.25), residues: 1176 helix: 1.53 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 82 TYR 0.017 0.001 TYR A 496 PHE 0.020 0.001 PHE A 357 TRP 0.017 0.001 TRP A 607 HIS 0.002 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00279 (10192) covalent geometry : angle 0.55835 (13816) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.57212 ( 4) hydrogen bonds : bond 0.03540 ( 664) hydrogen bonds : angle 4.10654 ( 1968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7826 (tp30) cc_final: 0.7449 (tm-30) REVERT: A 130 ASP cc_start: 0.8121 (m-30) cc_final: 0.7702 (t70) REVERT: A 210 ASP cc_start: 0.8389 (t70) cc_final: 0.7976 (t0) REVERT: A 213 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7619 (mtpt) REVERT: A 215 MET cc_start: 0.7909 (mmm) cc_final: 0.7654 (mmm) REVERT: A 219 ARG cc_start: 0.7119 (ttm-80) cc_final: 0.6815 (ttm-80) REVERT: A 532 MET cc_start: 0.8098 (mtp) cc_final: 0.7770 (mtp) REVERT: A 549 GLU cc_start: 0.8861 (tt0) cc_final: 0.8318 (tp30) REVERT: B 23 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7781 (tp30) REVERT: B 210 ASP cc_start: 0.8408 (t70) cc_final: 0.8141 (t70) REVERT: B 532 MET cc_start: 0.8100 (mtp) cc_final: 0.7745 (mtp) REVERT: B 549 GLU cc_start: 0.8842 (tt0) cc_final: 0.8284 (tp30) outliers start: 21 outliers final: 18 residues processed: 167 average time/residue: 0.0878 time to fit residues: 20.5194 Evaluate side-chains 164 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 90 optimal weight: 0.0370 chunk 110 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** 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 = 0.3989 r_free = 0.3989 target = 0.173637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113490 restraints weight = 12341.866| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.63 r_work: 0.3124 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10194 Z= 0.125 Angle : 0.557 9.025 13820 Z= 0.288 Chirality : 0.040 0.181 1506 Planarity : 0.004 0.032 1714 Dihedral : 4.049 21.861 1306 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.99 % Allowed : 26.14 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.22 (0.25), residues: 1176 helix: 1.69 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -1.96 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 82 TYR 0.018 0.001 TYR A 496 PHE 0.019 0.001 PHE B 357 TRP 0.016 0.001 TRP B 607 HIS 0.003 0.000 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00289 (10192) covalent geometry : angle 0.55691 (13816) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.49336 ( 4) hydrogen bonds : bond 0.03439 ( 664) hydrogen bonds : angle 4.01440 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2161.45 seconds wall clock time: 37 minutes 39.43 seconds (2259.43 seconds total)