Starting phenix.real_space_refine on Wed Aug 5 18:18:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z61_73830/08_2026/9z61_73830.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z61_73830/08_2026/9z61_73830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z61_73830/08_2026/9z61_73830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z61_73830/08_2026/9z61_73830.map" model { file = "/net/cci-nas-00/data/ceres_data/9z61_73830/08_2026/9z61_73830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z61_73830/08_2026/9z61_73830.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians S 27 5.16 5 Na 1 4.78 5 C 3510 2.51 5 N 874 2.21 5 O 977 1.98 5 H 5351 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10740 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 7209 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 20, 'TRANS': 452} Chain breaks: 1 Chain: "B" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1872 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1658 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.40, per 1000 atoms: 0.13 Number of scatterers: 10740 At special positions: 0 Unit cell: (79.75, 73.225, 119.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 Na 1 11.00 O 977 8.00 N 874 7.00 C 3510 6.00 H 5351 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " 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: 0.68 Conformation dependent library (CDL) restraints added in 173.6 milliseconds 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 7 sheets defined 59.6% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 80 through 100 removed outlier: 3.799A pdb=" N MET A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.944A pdb=" N SER A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 180 through 212 removed outlier: 4.401A pdb=" N HIS A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.966A pdb=" N MET A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 270 removed outlier: 3.604A pdb=" N ARG A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 364 removed outlier: 4.539A pdb=" N GLY A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 removed outlier: 3.867A pdb=" N VAL A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 384 through 402 removed outlier: 4.037A pdb=" N TYR A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 421 through 447 Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 451 through 474 Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.750A pdb=" N ARG A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 508 removed outlier: 4.208A pdb=" N ALA A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 508 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 522 through 550 Proline residue: A 532 - end of helix Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.910A pdb=" N SER A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP A 562 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 563 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.556A pdb=" N VAL C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.853A pdb=" N MET B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.502A pdb=" N ARG B 98 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 14 removed outlier: 3.510A pdb=" N LYS C 111 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 14 removed outlier: 3.510A pdb=" N LYS C 111 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 31 360 hydrogen bonds defined for protein. 996 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: 1.99 Time building geometry restraints manager: 0.93 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: 5345 1.03 - 1.23: 10 1.23 - 1.42: 2257 1.42 - 1.62: 3208 1.62 - 1.81: 42 Bond restraints: 10862 Sorted by residual: bond pdb=" N ILE A 504 " pdb=" CA ILE A 504 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.02e+00 bond pdb=" N ILE A 505 " pdb=" CA ILE A 505 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.41e-02 5.03e+03 6.72e+00 bond pdb=" N LEU A 506 " pdb=" CA LEU A 506 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.92e+00 bond pdb=" N LEU A 245 " pdb=" CA LEU A 245 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.17e-02 7.31e+03 5.34e+00 bond pdb=" N TYR A 503 " pdb=" CA TYR A 503 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.96e+00 ... (remaining 10857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 19608 5.95 - 11.89: 0 11.89 - 17.84: 0 17.84 - 23.78: 2 23.78 - 29.73: 4 Bond angle restraints: 19614 Sorted by residual: angle pdb="HG21 THR A 436 " pdb=" CG2 THR A 436 " pdb="HG22 THR A 436 " ideal model delta sigma weight residual 109.00 79.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb="HG22 THR A 436 " pdb=" CG2 THR A 436 " pdb="HG23 THR A 436 " ideal model delta sigma weight residual 109.00 79.67 29.33 3.00e+00 1.11e-01 9.56e+01 angle pdb=" CB THR A 436 " pdb=" CG2 THR A 436 " pdb="HG21 THR A 436 " ideal model delta sigma weight residual 110.00 80.98 29.02 3.00e+00 1.11e-01 9.36e+01 angle pdb=" CB THR A 436 " pdb=" CG2 THR A 436 " pdb="HG23 THR A 436 " ideal model delta sigma weight residual 110.00 82.22 27.78 3.00e+00 1.11e-01 8.57e+01 angle pdb=" CB THR A 436 " pdb=" CG2 THR A 436 " pdb="HG22 THR A 436 " ideal model delta sigma weight residual 110.00 132.92 -22.92 3.00e+00 1.11e-01 5.84e+01 ... (remaining 19609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4535 17.83 - 35.67: 407 35.67 - 53.50: 155 53.50 - 71.33: 34 71.33 - 89.16: 4 Dihedral angle restraints: 5135 sinusoidal: 2755 harmonic: 2380 Sorted by residual: dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 321 " pdb=" CB CYS A 321 " ideal model delta sinusoidal sigma weight residual 93.00 62.54 30.46 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CB GLU C 59 " pdb=" CG GLU C 59 " pdb=" CD GLU C 59 " pdb=" OE1 GLU C 59 " ideal model delta sinusoidal sigma weight residual 0.00 89.16 -89.16 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ARG A 181 " pdb=" CB ARG A 181 " pdb=" CG ARG A 181 " pdb=" CD ARG A 181 " ideal model delta sinusoidal sigma weight residual -60.00 -118.83 58.83 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 627 0.031 - 0.062: 159 0.062 - 0.092: 75 0.092 - 0.123: 33 0.123 - 0.154: 3 Chirality restraints: 897 Sorted by residual: chirality pdb=" CA ILE A 504 " pdb=" N ILE A 504 " pdb=" C ILE A 504 " pdb=" CB ILE A 504 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE C 52 " pdb=" N ILE C 52 " pdb=" C ILE C 52 " pdb=" CB ILE C 52 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE A 505 " pdb=" N ILE A 505 " pdb=" C ILE A 505 " pdb=" CB ILE A 505 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 894 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 506 " -0.029 2.00e-02 2.50e+03 5.60e-02 3.14e+01 pdb=" N CYS A 507 " 0.096 2.00e-02 2.50e+03 pdb=" CA CYS A 507 " -0.025 2.00e-02 2.50e+03 pdb=" H CYS A 507 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 109 " -0.022 2.00e-02 2.50e+03 2.19e-02 7.20e+00 pdb=" CD GLN A 109 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN A 109 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN A 109 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 109 " 0.031 2.00e-02 2.50e+03 pdb="HE22 GLN A 109 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 506 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C LEU A 506 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 506 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 507 " -0.011 2.00e-02 2.50e+03 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 213 2.13 - 2.75: 19470 2.75 - 3.36: 31652 3.36 - 3.98: 39527 3.98 - 4.60: 61320 Nonbonded interactions: 152182 Sorted by model distance: nonbonded pdb=" OE1 GLU A 266 " pdb=" H GLU A 266 " model vdw 1.509 2.450 nonbonded pdb="HH11 ARG A 181 " pdb=" O ALA A 494 " model vdw 1.696 2.450 nonbonded pdb=" OG SER A 556 " pdb="HD21 ASN C 31 " model vdw 1.719 2.450 nonbonded pdb=" O GLU A 450 " pdb=" HG1 THR A 451 " model vdw 1.729 2.450 nonbonded pdb=" OD1 ASP C 30 " pdb=" H GLY C 72 " model vdw 1.747 2.450 ... (remaining 152177 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 group one per residue 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: 3.530 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.310 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: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 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 : 0.002 0.037 5514 Z= 0.137 Angle : 0.461 5.516 7515 Z= 0.257 Chirality : 0.038 0.154 897 Planarity : 0.004 0.064 927 Dihedral : 16.056 89.165 1928 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.68 % Allowed : 23.65 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 3.30 (0.34), residues: 697 helix: 3.69 (0.28), residues: 362 sheet: 1.48 (0.52), residues: 117 loop : -0.13 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 224 TYR 0.008 0.001 TYR A 503 PHE 0.006 0.001 PHE A 502 TRP 0.003 0.000 TRP A 523 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 ( 5511) covalent geometry : angle 0.46120 / 0.26 ( 7509) SS BOND : bond 0.00113 / 0.06 ( 3) SS BOND : angle 0.16797 / 0.06 ( 6) hydrogen bonds : bond 0.14423 / 9.37 ( 346) hydrogen bonds : angle 5.18095 / 3.86 ( 996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.246 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.7784 (pptt) cc_final: 0.7502 (mmtt) REVERT: A 497 ARG cc_start: 0.7321 (mtm180) cc_final: 0.7066 (mtm110) REVERT: B 11 LEU cc_start: 0.6755 (tm) cc_final: 0.5583 (pp) REVERT: C 37 MET cc_start: 0.8017 (tpp) cc_final: 0.7709 (tpp) REVERT: C 40 TYR cc_start: 0.7967 (m-80) cc_final: 0.7682 (m-80) REVERT: C 94 GLN cc_start: 0.7789 (pp30) cc_final: 0.7341 (pp30) outliers start: 4 outliers final: 2 residues processed: 194 average time/residue: 0.1579 time to fit residues: 38.9662 Evaluate side-chains 138 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 100 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.196658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.165769 restraints weight = 21787.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173418 restraints weight = 11619.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.178503 restraints weight = 7462.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.181854 restraints weight = 5353.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.183946 restraints weight = 4104.514| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5514 Z= 0.166 Angle : 0.525 4.978 7515 Z= 0.284 Chirality : 0.039 0.142 897 Planarity : 0.005 0.073 927 Dihedral : 4.054 45.022 746 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.70 % Allowed : 24.32 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.64 (0.33), residues: 697 helix: 2.95 (0.28), residues: 366 sheet: 1.24 (0.53), residues: 117 loop : -0.11 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 224 TYR 0.013 0.001 TYR C 53 PHE 0.013 0.001 PHE A 325 TRP 0.004 0.001 TRP B 50 HIS 0.004 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 5511) covalent geometry : angle 0.52405 / 0.28 ( 7509) SS BOND : bond 0.00409 / 0.21 ( 3) SS BOND : angle 1.00647 / 0.46 ( 6) hydrogen bonds : bond 0.03765 / 2.54 ( 346) hydrogen bonds : angle 4.80016 / 3.55 ( 996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 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: 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 217 LYS cc_start: 0.6409 (mmmt) cc_final: 0.6205 (mmmt) REVERT: A 437 THR cc_start: 0.5965 (p) cc_final: 0.5657 (p) REVERT: B 11 LEU cc_start: 0.6771 (tm) cc_final: 0.5635 (pp) REVERT: B 28 THR cc_start: 0.8519 (m) cc_final: 0.8236 (p) REVERT: C 40 TYR cc_start: 0.8272 (m-80) cc_final: 0.7835 (m-80) outliers start: 16 outliers final: 9 residues processed: 157 average time/residue: 0.1167 time to fit residues: 24.7624 Evaluate side-chains 144 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain C residue 41 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.212785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.183136 restraints weight = 22810.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.191314 restraints weight = 11195.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.196531 restraints weight = 6982.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.199796 restraints weight = 4893.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.202201 restraints weight = 3715.325| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5514 Z= 0.126 Angle : 0.479 4.931 7515 Z= 0.255 Chirality : 0.038 0.135 897 Planarity : 0.005 0.073 927 Dihedral : 3.803 41.908 744 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.53 % Allowed : 23.48 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.54 (0.33), residues: 697 helix: 2.90 (0.28), residues: 366 sheet: 0.97 (0.53), residues: 116 loop : -0.10 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 67 TYR 0.011 0.001 TYR C 53 PHE 0.009 0.001 PHE B 95 TRP 0.006 0.001 TRP A 561 HIS 0.004 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 5511) covalent geometry : angle 0.47927 / 0.26 ( 7509) SS BOND : bond 0.00299 / 0.15 ( 3) SS BOND : angle 0.55329 / 0.24 ( 6) hydrogen bonds : bond 0.03539 / 2.41 ( 346) hydrogen bonds : angle 4.52337 / 3.34 ( 996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.217 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 THR cc_start: 0.6108 (p) cc_final: 0.5825 (p) REVERT: B 10 GLU cc_start: 0.6811 (mp0) cc_final: 0.6401 (mp0) REVERT: B 11 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.5677 (pp) REVERT: B 28 THR cc_start: 0.8543 (m) cc_final: 0.8274 (p) REVERT: C 30 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6998 (t70) outliers start: 15 outliers final: 8 residues processed: 154 average time/residue: 0.1190 time to fit residues: 24.7952 Evaluate side-chains 145 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 41 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.207677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.176258 restraints weight = 22818.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.184479 restraints weight = 11555.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.189743 restraints weight = 7349.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.193210 restraints weight = 5281.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.195471 restraints weight = 4055.896| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5514 Z= 0.143 Angle : 0.513 6.589 7515 Z= 0.271 Chirality : 0.039 0.134 897 Planarity : 0.004 0.062 927 Dihedral : 3.866 38.863 744 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.04 % Allowed : 24.66 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.42 (0.33), residues: 697 helix: 2.77 (0.27), residues: 366 sheet: 1.10 (0.54), residues: 112 loop : -0.16 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 424 TYR 0.013 0.001 TYR C 53 PHE 0.012 0.001 PHE B 95 TRP 0.005 0.001 TRP A 561 HIS 0.005 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5511) covalent geometry : angle 0.51310 / 0.27 ( 7509) SS BOND : bond 0.00355 / 0.18 ( 3) SS BOND : angle 0.70996 / 0.30 ( 6) hydrogen bonds : bond 0.03461 / 2.35 ( 346) hydrogen bonds : angle 4.46250 / 3.30 ( 996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.268 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ILE cc_start: 0.7338 (mt) cc_final: 0.7026 (mt) REVERT: A 392 LEU cc_start: 0.8197 (tp) cc_final: 0.7960 (tp) REVERT: A 437 THR cc_start: 0.6504 (p) cc_final: 0.6270 (p) REVERT: A 509 PHE cc_start: 0.7650 (t80) cc_final: 0.6935 (m-80) REVERT: B 10 GLU cc_start: 0.6928 (mp0) cc_final: 0.6598 (mp0) REVERT: B 28 THR cc_start: 0.8574 (m) cc_final: 0.8281 (p) REVERT: B 104 SER cc_start: 0.9267 (t) cc_final: 0.8845 (p) outliers start: 18 outliers final: 11 residues processed: 147 average time/residue: 0.1112 time to fit residues: 22.4823 Evaluate side-chains 138 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.203199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.171238 restraints weight = 22843.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179266 restraints weight = 12035.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.184293 restraints weight = 7801.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.187711 restraints weight = 5708.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.190085 restraints weight = 4456.225| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5514 Z= 0.161 Angle : 0.509 5.340 7515 Z= 0.275 Chirality : 0.038 0.135 897 Planarity : 0.004 0.052 927 Dihedral : 3.665 14.555 742 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.87 % Allowed : 24.49 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.25 (0.33), residues: 697 helix: 2.68 (0.27), residues: 366 sheet: 0.74 (0.53), residues: 115 loop : -0.16 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.009 0.001 TYR C 53 PHE 0.015 0.001 PHE A 196 TRP 0.006 0.001 TRP A 561 HIS 0.006 0.002 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 5511) covalent geometry : angle 0.50874 / 0.27 ( 7509) SS BOND : bond 0.00430 / 0.22 ( 3) SS BOND : angle 0.65801 / 0.26 ( 6) hydrogen bonds : bond 0.03641 / 2.48 ( 346) hydrogen bonds : angle 4.41726 / 3.25 ( 996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.232 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ILE cc_start: 0.7580 (mt) cc_final: 0.7301 (mt) REVERT: A 509 PHE cc_start: 0.7688 (t80) cc_final: 0.6931 (m-80) REVERT: B 10 GLU cc_start: 0.7101 (mp0) cc_final: 0.6740 (mp0) REVERT: B 28 THR cc_start: 0.8573 (m) cc_final: 0.8266 (p) REVERT: B 104 SER cc_start: 0.9363 (t) cc_final: 0.8994 (p) outliers start: 17 outliers final: 14 residues processed: 150 average time/residue: 0.1190 time to fit residues: 24.4306 Evaluate side-chains 142 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.203001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170831 restraints weight = 23032.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.178888 restraints weight = 11801.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.184084 restraints weight = 7619.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.187501 restraints weight = 5527.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.189840 restraints weight = 4314.133| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5514 Z= 0.139 Angle : 0.493 5.633 7515 Z= 0.266 Chirality : 0.038 0.144 897 Planarity : 0.004 0.050 927 Dihedral : 3.626 14.744 742 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.04 % Allowed : 24.32 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.33 (0.34), residues: 697 helix: 2.73 (0.28), residues: 365 sheet: 0.90 (0.52), residues: 126 loop : -0.24 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 424 TYR 0.009 0.001 TYR C 53 PHE 0.011 0.001 PHE B 95 TRP 0.006 0.001 TRP A 561 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 5511) covalent geometry : angle 0.49343 / 0.27 ( 7509) SS BOND : bond 0.00353 / 0.18 ( 3) SS BOND : angle 0.57466 / 0.24 ( 6) hydrogen bonds : bond 0.03528 / 2.43 ( 346) hydrogen bonds : angle 4.34573 / 3.20 ( 996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.241 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: A 107 ILE cc_start: 0.7565 (mt) cc_final: 0.7248 (mt) REVERT: A 509 PHE cc_start: 0.7715 (t80) cc_final: 0.7045 (m-80) REVERT: A 576 ARG cc_start: 0.7646 (mtp180) cc_final: 0.7114 (ttm170) REVERT: B 28 THR cc_start: 0.8515 (m) cc_final: 0.8228 (p) REVERT: B 104 SER cc_start: 0.9358 (t) cc_final: 0.9027 (p) outliers start: 18 outliers final: 16 residues processed: 145 average time/residue: 0.1199 time to fit residues: 23.8800 Evaluate side-chains 140 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.202732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170428 restraints weight = 22786.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.178318 restraints weight = 11807.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.183562 restraints weight = 7685.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.187080 restraints weight = 5568.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.189103 restraints weight = 4326.391| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5514 Z= 0.124 Angle : 0.495 5.776 7515 Z= 0.265 Chirality : 0.038 0.131 897 Planarity : 0.004 0.048 927 Dihedral : 3.660 15.269 742 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.86 % Allowed : 25.34 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.33 (0.34), residues: 697 helix: 2.80 (0.28), residues: 365 sheet: 0.81 (0.51), residues: 126 loop : -0.31 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 484 TYR 0.009 0.001 TYR C 53 PHE 0.016 0.001 PHE A 196 TRP 0.007 0.001 TRP A 561 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 5511) covalent geometry : angle 0.49448 / 0.26 ( 7509) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 0.81171 / 0.30 ( 6) hydrogen bonds : bond 0.03468 / 2.39 ( 346) hydrogen bonds : angle 4.25920 / 3.14 ( 996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.177 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 96 PHE cc_start: 0.9038 (m-80) cc_final: 0.8700 (m-80) REVERT: A 107 ILE cc_start: 0.7723 (mt) cc_final: 0.7459 (mt) REVERT: A 473 TRP cc_start: 0.7464 (m100) cc_final: 0.7047 (m100) REVERT: A 509 PHE cc_start: 0.7753 (t80) cc_final: 0.6973 (m-80) REVERT: A 574 TRP cc_start: 0.8347 (m100) cc_final: 0.7947 (m-10) REVERT: A 576 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7256 (ttm170) REVERT: B 28 THR cc_start: 0.8565 (m) cc_final: 0.8213 (p) REVERT: B 104 SER cc_start: 0.9357 (t) cc_final: 0.9008 (p) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.1070 time to fit residues: 20.0466 Evaluate side-chains 135 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 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 = 0.4480 r_free = 0.4480 target = 0.204775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.170290 restraints weight = 23166.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.178558 restraints weight = 12148.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.183886 restraints weight = 7925.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.187459 restraints weight = 5823.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.190100 restraints weight = 4607.075| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5514 Z= 0.128 Angle : 0.500 5.910 7515 Z= 0.268 Chirality : 0.038 0.130 897 Planarity : 0.004 0.047 927 Dihedral : 3.642 15.429 742 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.87 % Allowed : 25.17 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.26 (0.34), residues: 697 helix: 2.80 (0.28), residues: 365 sheet: 0.73 (0.51), residues: 126 loop : -0.43 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 484 TYR 0.009 0.001 TYR B 60 PHE 0.012 0.001 PHE A 196 TRP 0.007 0.001 TRP A 561 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5511) covalent geometry : angle 0.50014 / 0.27 ( 7509) SS BOND : bond 0.00238 / 0.12 ( 3) SS BOND : angle 0.68970 / 0.26 ( 6) hydrogen bonds : bond 0.03466 / 2.39 ( 346) hydrogen bonds : angle 4.23040 / 3.12 ( 996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.161 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 96 PHE cc_start: 0.9056 (m-80) cc_final: 0.8762 (m-80) REVERT: A 107 ILE cc_start: 0.7790 (mt) cc_final: 0.7538 (mt) REVERT: A 509 PHE cc_start: 0.7798 (t80) cc_final: 0.7055 (m-80) REVERT: A 574 TRP cc_start: 0.8337 (m100) cc_final: 0.7952 (m-10) REVERT: A 576 ARG cc_start: 0.7783 (mtp180) cc_final: 0.7221 (ttm170) REVERT: B 28 THR cc_start: 0.8568 (m) cc_final: 0.8226 (p) REVERT: B 98 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7171 (ppt90) REVERT: B 104 SER cc_start: 0.9372 (t) cc_final: 0.9028 (p) outliers start: 17 outliers final: 15 residues processed: 138 average time/residue: 0.1101 time to fit residues: 20.9347 Evaluate side-chains 142 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.201463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.169381 restraints weight = 22663.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.177404 restraints weight = 11719.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.182446 restraints weight = 7534.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.185814 restraints weight = 5510.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.187881 restraints weight = 4307.469| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5514 Z= 0.120 Angle : 0.494 5.956 7515 Z= 0.264 Chirality : 0.038 0.131 897 Planarity : 0.004 0.045 927 Dihedral : 3.624 15.720 742 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.20 % Allowed : 25.84 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.27 (0.34), residues: 697 helix: 2.86 (0.28), residues: 365 sheet: 0.67 (0.51), residues: 126 loop : -0.50 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.013 0.001 TYR B 106 PHE 0.011 0.001 PHE C 32 TRP 0.008 0.001 TRP A 561 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 5511) covalent geometry : angle 0.49419 / 0.26 ( 7509) SS BOND : bond 0.00227 / 0.11 ( 3) SS BOND : angle 0.65733 / 0.24 ( 6) hydrogen bonds : bond 0.03397 / 2.35 ( 346) hydrogen bonds : angle 4.18563 / 3.09 ( 996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.267 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 96 PHE cc_start: 0.9065 (m-80) cc_final: 0.8740 (m-80) REVERT: A 107 ILE cc_start: 0.7817 (mt) cc_final: 0.7580 (mt) REVERT: A 509 PHE cc_start: 0.7783 (t80) cc_final: 0.7005 (m-80) REVERT: A 574 TRP cc_start: 0.8347 (m100) cc_final: 0.7975 (m-10) REVERT: A 576 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7273 (ttm170) REVERT: B 28 THR cc_start: 0.8564 (m) cc_final: 0.8207 (p) REVERT: B 104 SER cc_start: 0.9342 (t) cc_final: 0.9063 (p) outliers start: 13 outliers final: 12 residues processed: 134 average time/residue: 0.1044 time to fit residues: 19.2882 Evaluate side-chains 137 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.204940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.170853 restraints weight = 23028.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.179189 restraints weight = 11905.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.184466 restraints weight = 7723.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.188140 restraints weight = 5673.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.190587 restraints weight = 4445.460| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5514 Z= 0.115 Angle : 0.490 5.987 7515 Z= 0.262 Chirality : 0.038 0.131 897 Planarity : 0.004 0.046 927 Dihedral : 3.603 15.907 742 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.20 % Allowed : 26.18 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.29 (0.34), residues: 697 helix: 2.90 (0.28), residues: 365 sheet: 0.66 (0.51), residues: 126 loop : -0.52 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 497 TYR 0.014 0.001 TYR B 60 PHE 0.008 0.001 PHE C 91 TRP 0.009 0.001 TRP A 561 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 5511) covalent geometry : angle 0.48959 / 0.26 ( 7509) SS BOND : bond 0.00208 / 0.10 ( 3) SS BOND : angle 0.58501 / 0.22 ( 6) hydrogen bonds : bond 0.03359 / 2.32 ( 346) hydrogen bonds : angle 4.14793 / 3.06 ( 996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.268 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: A 96 PHE cc_start: 0.9062 (m-80) cc_final: 0.8778 (m-80) REVERT: A 107 ILE cc_start: 0.7736 (mt) cc_final: 0.7490 (mt) REVERT: A 473 TRP cc_start: 0.7378 (m100) cc_final: 0.6962 (m100) REVERT: A 509 PHE cc_start: 0.7765 (t80) cc_final: 0.7075 (m-80) REVERT: A 574 TRP cc_start: 0.8284 (m100) cc_final: 0.7971 (m-10) REVERT: A 576 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7186 (ttm170) REVERT: B 28 THR cc_start: 0.8533 (m) cc_final: 0.8198 (p) REVERT: B 98 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7421 (ppt90) REVERT: B 104 SER cc_start: 0.9347 (t) cc_final: 0.9057 (p) outliers start: 13 outliers final: 12 residues processed: 134 average time/residue: 0.1186 time to fit residues: 22.0836 Evaluate side-chains 137 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 375 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.199234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.166999 restraints weight = 22982.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.174891 restraints weight = 12053.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180021 restraints weight = 7822.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.183306 restraints weight = 5710.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.185618 restraints weight = 4514.561| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5514 Z= 0.138 Angle : 0.505 5.575 7515 Z= 0.272 Chirality : 0.038 0.128 897 Planarity : 0.004 0.046 927 Dihedral : 3.671 16.230 742 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.36 % Allowed : 26.35 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.12 (0.34), residues: 697 helix: 2.79 (0.27), residues: 365 sheet: 0.49 (0.51), residues: 126 loop : -0.58 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.008 0.001 TYR A 503 PHE 0.011 0.001 PHE C 91 TRP 0.009 0.001 TRP A 561 HIS 0.005 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 5511) covalent geometry : angle 0.50440 / 0.27 ( 7509) SS BOND : bond 0.00300 / 0.15 ( 3) SS BOND : angle 0.71609 / 0.26 ( 6) hydrogen bonds : bond 0.03500 / 2.43 ( 346) hydrogen bonds : angle 4.20917 / 3.10 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1905.39 seconds wall clock time: 33 minutes 2.75 seconds (1982.75 seconds total)