Starting phenix.real_space_refine on Wed Aug 5 18:17:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z63_73832/08_2026/9z63_73832_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z63_73832/08_2026/9z63_73832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z63_73832/08_2026/9z63_73832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z63_73832/08_2026/9z63_73832.map" model { file = "/net/cci-nas-00/data/ceres_data/9z63_73832/08_2026/9z63_73832_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z63_73832/08_2026/9z63_73832_trim.cif" } resolution = 3.02 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 Na 3 4.78 5 C 3511 2.51 5 N 874 2.21 5 O 982 1.98 5 H 5342 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 7200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 7200 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 10 Unusual residues: {' NA': 3, 'PPF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.99, per 1000 atoms: 0.19 Number of scatterers: 10740 At special positions: 0 Unit cell: (79.75, 73.225, 118.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 27 16.00 P 1 15.00 Na 3 11.00 O 982 8.00 N 874 7.00 C 3511 6.00 H 5342 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=2.04 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: 1.00 Conformation dependent library (CDL) restraints added in 274.4 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 60.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 80 through 100 removed outlier: 3.814A pdb=" N MET A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 111 through 115 removed outlier: 5.151A pdb=" N LEU A 114 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.939A 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 167 through 177 removed outlier: 3.872A pdb=" N THR A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 212 removed outlier: 4.345A pdb=" N HIS A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.950A 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: 3.888A pdb=" N MET A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 270 removed outlier: 3.526A pdb=" N ARG A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 Processing helix chain 'A' and resid 365 through 376 removed outlier: 3.905A pdb=" N VAL A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.506A pdb=" N ALA A 383 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 402 removed outlier: 4.067A pdb=" N TYR A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 421 through 446 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: 3.784A pdb=" N ARG A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 4.152A pdb=" N ALA A 501 " --> pdb=" O ARG A 497 " (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 555 through 564 removed outlier: 4.129A pdb=" N SER A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP A 562 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.439A 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: 3.647A 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: 6.723A pdb=" N MET B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.733A 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: 4.333A 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: 6.981A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.463A 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: 3.548A 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 31 365 hydrogen bonds defined for protein. 1014 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: 1.85 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5336 1.04 - 1.25: 763 1.25 - 1.45: 1628 1.45 - 1.66: 3089 1.66 - 1.86: 43 Bond restraints: 10859 Sorted by residual: bond pdb=" N ASP A 377 " pdb=" CA ASP A 377 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.17e-02 7.31e+03 8.59e+00 bond pdb=" N VAL A 577 " pdb=" CA VAL A 577 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.21e-02 6.83e+03 7.28e+00 bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.457 1.484 -0.028 1.24e-02 6.50e+03 5.05e+00 bond pdb=" N VAL A 577 " pdb=" H VAL A 577 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" N SER A 258 " pdb=" CA SER A 258 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.49e+00 ... (remaining 10854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 19591 5.96 - 11.91: 5 11.91 - 17.87: 0 17.87 - 23.83: 2 23.83 - 29.78: 4 Bond angle restraints: 19602 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 79.22 29.78 3.00e+00 1.11e-01 9.86e+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 79.65 29.35 3.00e+00 1.11e-01 9.57e+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 80.97 29.03 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 82.27 27.73 3.00e+00 1.11e-01 8.55e+01 angle pdb=" CB THR A 436 " pdb=" CG2 THR A 436 " pdb="HG22 THR A 436 " ideal model delta sigma weight residual 110.00 132.90 -22.90 3.00e+00 1.11e-01 5.83e+01 ... (remaining 19597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4545 17.84 - 35.69: 392 35.69 - 53.53: 149 53.53 - 71.37: 42 71.37 - 89.21: 6 Dihedral angle restraints: 5134 sinusoidal: 2754 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 38.11 54.89 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 66.71 26.29 1 1.00e+01 1.00e-02 9.93e+00 dihedral pdb=" CG ARG A 67 " pdb=" CD ARG A 67 " pdb=" NE ARG A 67 " pdb=" CZ ARG A 67 " ideal model delta sinusoidal sigma weight residual 180.00 137.15 42.85 2 1.50e+01 4.44e-03 9.87e+00 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 666 0.036 - 0.071: 162 0.071 - 0.107: 50 0.107 - 0.142: 16 0.142 - 0.177: 3 Chirality restraints: 897 Sorted by residual: chirality pdb=" CA MET A 445 " pdb=" N MET A 445 " pdb=" C MET A 445 " pdb=" CB MET A 445 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA VAL A 577 " pdb=" N VAL A 577 " pdb=" C VAL A 577 " pdb=" CB VAL A 577 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA LEU B 4 " pdb=" N LEU B 4 " pdb=" C LEU B 4 " pdb=" CB LEU B 4 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 894 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 3 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLN B 3 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN B 3 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 4 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 577 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" N VAL A 578 " -0.028 2.00e-02 2.50e+03 pdb=" CA VAL A 578 " 0.007 2.00e-02 2.50e+03 pdb=" H VAL A 578 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 258 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" N GLY A 259 " 0.027 2.00e-02 2.50e+03 pdb=" CA GLY A 259 " -0.007 2.00e-02 2.50e+03 pdb=" H GLY A 259 " -0.012 2.00e-02 2.50e+03 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1488 2.26 - 2.84: 24520 2.84 - 3.43: 28844 3.43 - 4.01: 39681 4.01 - 4.60: 59962 Nonbonded interactions: 154495 Sorted by model distance: nonbonded pdb=" O LEU A 506 " pdb=" H LEU A 511 " model vdw 1.672 2.450 nonbonded pdb="HE21 GLN A 547 " pdb=" O LEU A 558 " model vdw 1.673 2.450 nonbonded pdb="HH11 ARG A 181 " pdb=" O ALA A 494 " model vdw 1.722 2.450 nonbonded pdb=" O GLU A 450 " pdb=" HG1 THR A 451 " model vdw 1.725 2.450 nonbonded pdb=" O LEU A 205 " pdb=" H GLU A 209 " model vdw 1.728 2.450 ... (remaining 154490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.730 Find NCS groups from input model: 0.040 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 0.034 5520 Z= 0.144 Angle : 0.521 9.353 7524 Z= 0.285 Chirality : 0.038 0.177 897 Planarity : 0.004 0.047 928 Dihedral : 16.295 89.214 1929 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.68 % Allowed : 25.00 % Favored : 74.32 % 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: 2.86 (0.33), residues: 697 helix: 3.21 (0.27), residues: 365 sheet: 1.54 (0.51), residues: 116 loop : -0.31 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 484 TYR 0.007 0.001 TYR C 40 PHE 0.014 0.001 PHE A 108 TRP 0.004 0.001 TRP A 276 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 ( 5517) covalent geometry : angle 0.51992 / 0.28 ( 7518) SS BOND : bond 0.00429 / 0.22 ( 3) SS BOND : angle 1.13949 / 0.62 ( 6) hydrogen bonds : bond 0.12760 / 8.49 ( 350) hydrogen bonds : angle 5.66850 / 4.11 ( 1014) *********************** 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 81 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 THR cc_start: 0.8488 (t) cc_final: 0.8287 (m) REVERT: A 527 MET cc_start: 0.6039 (tmm) cc_final: 0.5338 (mmt) REVERT: A 537 LEU cc_start: 0.6899 (mm) cc_final: 0.6556 (tp) REVERT: A 548 LYS cc_start: 0.7283 (mttt) cc_final: 0.6527 (mptt) REVERT: B 13 LYS cc_start: 0.7277 (ttpt) cc_final: 0.7022 (ttmm) REVERT: B 107 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8202 (mmt-90) outliers start: 4 outliers final: 4 residues processed: 81 average time/residue: 0.1397 time to fit residues: 15.1962 Evaluate side-chains 66 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain C residue 41 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.200930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.179620 restraints weight = 14567.807| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.32 r_work: 0.3489 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5520 Z= 0.129 Angle : 0.484 5.039 7524 Z= 0.253 Chirality : 0.039 0.158 897 Planarity : 0.004 0.036 928 Dihedral : 4.589 50.768 750 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.03 % Allowed : 21.79 % Favored : 76.18 % 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: 2.51 (0.33), residues: 697 helix: 2.83 (0.27), residues: 367 sheet: 1.48 (0.51), residues: 117 loop : -0.39 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 484 TYR 0.015 0.001 TYR C 53 PHE 0.012 0.001 PHE A 509 TRP 0.009 0.001 TRP B 112 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 5517) covalent geometry : angle 0.48050 / 0.25 ( 7518) SS BOND : bond 0.00580 / 0.30 ( 3) SS BOND : angle 1.96643 / 1.06 ( 6) hydrogen bonds : bond 0.03805 / 2.58 ( 350) hydrogen bonds : angle 4.88974 / 3.56 ( 1014) *********************** 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 81 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.5890 (tmm) cc_final: 0.5299 (mmt) REVERT: A 537 LEU cc_start: 0.6880 (mm) cc_final: 0.6547 (tp) REVERT: A 548 LYS cc_start: 0.7415 (mttt) cc_final: 0.6557 (mptt) REVERT: B 63 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7258 (t0) REVERT: B 107 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8294 (mmt-90) outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 0.1553 time to fit residues: 16.3973 Evaluate side-chains 72 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 109 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.194331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172026 restraints weight = 14739.076| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.36 r_work: 0.3390 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5520 Z= 0.138 Angle : 0.477 5.017 7524 Z= 0.254 Chirality : 0.039 0.148 897 Planarity : 0.004 0.033 928 Dihedral : 4.464 52.949 746 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.72 % Allowed : 19.59 % Favored : 76.69 % 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: 2.22 (0.33), residues: 697 helix: 2.53 (0.27), residues: 366 sheet: 1.34 (0.51), residues: 122 loop : -0.40 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.010 0.001 TYR C 53 PHE 0.007 0.001 PHE B 64 TRP 0.007 0.001 TRP B 47 HIS 0.004 0.002 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 5517) covalent geometry : angle 0.47469 / 0.25 ( 7518) SS BOND : bond 0.00442 / 0.23 ( 3) SS BOND : angle 1.58441 / 0.84 ( 6) hydrogen bonds : bond 0.04085 / 2.77 ( 350) hydrogen bonds : angle 4.79170 / 3.48 ( 1014) *********************** 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 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.5976 (tmm) cc_final: 0.5349 (mmt) REVERT: A 537 LEU cc_start: 0.6947 (mm) cc_final: 0.6615 (tp) REVERT: A 548 LYS cc_start: 0.7717 (mttt) cc_final: 0.6899 (mptt) REVERT: B 63 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7341 (t0) REVERT: B 99 ASN cc_start: 0.7782 (m-40) cc_final: 0.7050 (m-40) REVERT: B 107 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8265 (mmt-90) REVERT: C 74 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6189 (m-30) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 0.1240 time to fit residues: 14.1396 Evaluate side-chains 82 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.190390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164976 restraints weight = 14520.296| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.45 r_work: 0.3506 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.004 0.056 5520 Z= 0.157 Angle : 0.488 5.042 7524 Z= 0.260 Chirality : 0.039 0.143 897 Planarity : 0.004 0.032 928 Dihedral : 4.732 57.270 746 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.04 % Allowed : 19.76 % Favored : 77.20 % 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: 1.89 (0.33), residues: 697 helix: 2.32 (0.27), residues: 367 sheet: 1.04 (0.50), residues: 121 loop : -0.56 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.011 0.001 TYR C 53 PHE 0.007 0.001 PHE B 95 TRP 0.008 0.001 TRP B 47 HIS 0.006 0.002 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 5517) covalent geometry : angle 0.48661 / 0.26 ( 7518) SS BOND : bond 0.00411 / 0.21 ( 3) SS BOND : angle 1.41098 / 0.74 ( 6) hydrogen bonds : bond 0.04056 / 2.77 ( 350) hydrogen bonds : angle 4.80498 / 3.49 ( 1014) *********************** 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 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ILE cc_start: 0.8133 (mt) cc_final: 0.7819 (mt) REVERT: A 474 TYR cc_start: 0.8105 (t80) cc_final: 0.7412 (t80) REVERT: A 527 MET cc_start: 0.6175 (tmm) cc_final: 0.5493 (mmt) REVERT: A 537 LEU cc_start: 0.7009 (mm) cc_final: 0.6664 (tp) REVERT: A 548 LYS cc_start: 0.7916 (mttt) cc_final: 0.7104 (mptt) REVERT: B 63 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7372 (t0) REVERT: B 99 ASN cc_start: 0.7993 (m-40) cc_final: 0.7375 (m-40) REVERT: B 107 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8347 (mmt-90) REVERT: C 109 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5447 (mt-10) outliers start: 18 outliers final: 11 residues processed: 84 average time/residue: 0.1251 time to fit residues: 14.2037 Evaluate side-chains 80 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 109 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.188656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163625 restraints weight = 14585.048| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.44 r_work: 0.3491 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5520 Z= 0.138 Angle : 0.471 4.823 7524 Z= 0.251 Chirality : 0.039 0.138 897 Planarity : 0.004 0.031 928 Dihedral : 4.788 59.571 746 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.04 % Allowed : 19.93 % Favored : 77.03 % 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: 1.84 (0.33), residues: 697 helix: 2.31 (0.27), residues: 368 sheet: 0.88 (0.50), residues: 121 loop : -0.58 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.010 0.001 TYR C 53 PHE 0.007 0.001 PHE A 464 TRP 0.008 0.001 TRP B 47 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5517) covalent geometry : angle 0.46981 / 0.25 ( 7518) SS BOND : bond 0.00344 / 0.18 ( 3) SS BOND : angle 1.17986 / 0.62 ( 6) hydrogen bonds : bond 0.03934 / 2.68 ( 350) hydrogen bonds : angle 4.74536 / 3.44 ( 1014) *********************** 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 85 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.7288 (ppp) cc_final: 0.6960 (ptm) REVERT: A 527 MET cc_start: 0.6039 (tmm) cc_final: 0.5395 (mmt) REVERT: A 530 LEU cc_start: 0.8153 (mp) cc_final: 0.7950 (mp) REVERT: A 537 LEU cc_start: 0.6957 (mm) cc_final: 0.6593 (tp) REVERT: A 548 LYS cc_start: 0.7841 (mttt) cc_final: 0.7003 (mptt) REVERT: B 63 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7405 (t0) REVERT: B 99 ASN cc_start: 0.8049 (m-40) cc_final: 0.7331 (m-40) REVERT: B 107 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8268 (mmt-90) REVERT: C 74 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6333 (m-30) REVERT: C 109 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5367 (mt-10) outliers start: 18 outliers final: 14 residues processed: 80 average time/residue: 0.1185 time to fit residues: 12.9859 Evaluate side-chains 83 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 109 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 chunk 48 optimal weight: 0.0020 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.167363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.140298 restraints weight = 15496.555| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.55 r_work: 0.3312 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5520 Z= 0.103 Angle : 0.441 4.440 7524 Z= 0.235 Chirality : 0.038 0.134 897 Planarity : 0.004 0.030 928 Dihedral : 4.629 55.899 746 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.03 % Allowed : 21.11 % Favored : 76.86 % 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: 1.96 (0.33), residues: 697 helix: 2.48 (0.27), residues: 368 sheet: 0.89 (0.50), residues: 121 loop : -0.65 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.008 0.001 TYR C 53 PHE 0.006 0.001 PHE A 464 TRP 0.006 0.001 TRP A 473 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 5517) covalent geometry : angle 0.44045 / 0.23 ( 7518) SS BOND : bond 0.00267 / 0.14 ( 3) SS BOND : angle 0.97257 / 0.50 ( 6) hydrogen bonds : bond 0.03582 / 2.44 ( 350) hydrogen bonds : angle 4.58379 / 3.32 ( 1014) *********************** 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 78 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.7249 (ppp) cc_final: 0.6773 (ptm) REVERT: A 527 MET cc_start: 0.5974 (tmm) cc_final: 0.5288 (mmt) REVERT: A 537 LEU cc_start: 0.6846 (mm) cc_final: 0.6471 (tp) REVERT: A 548 LYS cc_start: 0.7702 (mttt) cc_final: 0.6800 (mptt) REVERT: B 99 ASN cc_start: 0.7962 (m-40) cc_final: 0.6918 (m-40) REVERT: B 107 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8248 (mmt-90) REVERT: C 18 ARG cc_start: 0.7324 (ptt90) cc_final: 0.7079 (ptt90) REVERT: C 74 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6290 (m-30) REVERT: C 97 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7419 (pt0) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.1629 time to fit residues: 16.1932 Evaluate side-chains 74 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.164434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.134691 restraints weight = 15464.145| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.66 r_work: 0.3243 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5520 Z= 0.135 Angle : 0.463 4.812 7524 Z= 0.247 Chirality : 0.039 0.138 897 Planarity : 0.004 0.030 928 Dihedral : 4.687 53.341 746 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.87 % Allowed : 20.10 % Favored : 77.03 % 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: 1.84 (0.33), residues: 697 helix: 2.39 (0.27), residues: 368 sheet: 0.76 (0.50), residues: 121 loop : -0.67 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.010 0.001 TYR C 53 PHE 0.006 0.001 PHE A 464 TRP 0.008 0.001 TRP B 47 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 5517) covalent geometry : angle 0.46246 / 0.25 ( 7518) SS BOND : bond 0.00280 / 0.14 ( 3) SS BOND : angle 0.83610 / 0.42 ( 6) hydrogen bonds : bond 0.03847 / 2.64 ( 350) hydrogen bonds : angle 4.65444 / 3.37 ( 1014) *********************** 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 88 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6018 (tmm) cc_final: 0.5300 (mmt) REVERT: A 537 LEU cc_start: 0.6840 (mm) cc_final: 0.6457 (tp) REVERT: A 548 LYS cc_start: 0.7731 (mttt) cc_final: 0.6815 (mptt) REVERT: B 19 LYS cc_start: 0.8278 (tptm) cc_final: 0.8006 (tptm) REVERT: B 99 ASN cc_start: 0.8050 (m-40) cc_final: 0.7061 (m-40) REVERT: B 107 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8302 (mmt-90) REVERT: C 18 ARG cc_start: 0.7364 (ptt90) cc_final: 0.7129 (ptt90) REVERT: C 74 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6389 (m-30) REVERT: C 109 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5397 (mt-10) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.1514 time to fit residues: 17.2019 Evaluate side-chains 82 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 109 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.3980 chunk 15 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.164669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.136364 restraints weight = 15403.236| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.59 r_work: 0.3259 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5520 Z= 0.125 Angle : 0.461 4.565 7524 Z= 0.245 Chirality : 0.038 0.138 897 Planarity : 0.004 0.030 928 Dihedral : 4.646 51.278 746 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.03 % Allowed : 21.11 % Favored : 76.86 % 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: 1.77 (0.33), residues: 697 helix: 2.36 (0.27), residues: 369 sheet: 0.71 (0.49), residues: 121 loop : -0.75 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.008 0.001 TYR C 53 PHE 0.006 0.001 PHE A 464 TRP 0.008 0.001 TRP B 47 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 5517) covalent geometry : angle 0.46052 / 0.24 ( 7518) SS BOND : bond 0.00252 / 0.13 ( 3) SS BOND : angle 0.79903 / 0.39 ( 6) hydrogen bonds : bond 0.03754 / 2.56 ( 350) hydrogen bonds : angle 4.63483 / 3.35 ( 1014) *********************** 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 82 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6051 (tmm) cc_final: 0.5298 (mmt) REVERT: A 537 LEU cc_start: 0.6883 (mm) cc_final: 0.6501 (tp) REVERT: A 548 LYS cc_start: 0.7754 (mttt) cc_final: 0.6856 (mptt) REVERT: B 99 ASN cc_start: 0.8049 (m-40) cc_final: 0.6963 (m-40) REVERT: B 107 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8316 (mmt-90) REVERT: C 18 ARG cc_start: 0.7367 (ptt90) cc_final: 0.7145 (ptt90) REVERT: C 74 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6425 (m-30) outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 0.1471 time to fit residues: 15.6461 Evaluate side-chains 81 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 74 ASP 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: 0.1980 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.164594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.137170 restraints weight = 15312.165| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.55 r_work: 0.3268 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5520 Z= 0.117 Angle : 0.456 4.529 7524 Z= 0.243 Chirality : 0.038 0.137 897 Planarity : 0.004 0.030 928 Dihedral : 4.603 49.076 746 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.53 % Allowed : 20.44 % Favored : 77.03 % 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: 1.78 (0.33), residues: 697 helix: 2.38 (0.27), residues: 369 sheet: 0.90 (0.51), residues: 111 loop : -0.83 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.010 0.001 TYR B 80 PHE 0.007 0.001 PHE A 108 TRP 0.007 0.001 TRP B 47 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 5517) covalent geometry : angle 0.45533 / 0.24 ( 7518) SS BOND : bond 0.00242 / 0.12 ( 3) SS BOND : angle 0.79786 / 0.38 ( 6) hydrogen bonds : bond 0.03677 / 2.50 ( 350) hydrogen bonds : angle 4.60117 / 3.33 ( 1014) *********************** 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 82 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6052 (tmm) cc_final: 0.5310 (mmt) REVERT: A 548 LYS cc_start: 0.7718 (mttt) cc_final: 0.6796 (mptt) REVERT: B 4 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6566 (mt) REVERT: B 99 ASN cc_start: 0.8028 (m-40) cc_final: 0.6946 (m-40) REVERT: B 107 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8278 (mmt-90) REVERT: C 18 ARG cc_start: 0.7367 (ptt90) cc_final: 0.7160 (ptt90) REVERT: C 74 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6379 (m-30) REVERT: C 109 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5416 (mt-10) outliers start: 15 outliers final: 9 residues processed: 79 average time/residue: 0.1396 time to fit residues: 14.9292 Evaluate side-chains 78 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 109 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.164842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.136661 restraints weight = 15315.799| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.59 r_work: 0.3257 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5520 Z= 0.109 Angle : 0.453 4.387 7524 Z= 0.240 Chirality : 0.038 0.156 897 Planarity : 0.004 0.030 928 Dihedral : 4.531 48.771 746 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.69 % Allowed : 21.11 % Favored : 77.20 % 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: 1.84 (0.32), residues: 697 helix: 2.41 (0.27), residues: 368 sheet: 1.08 (0.51), residues: 108 loop : -0.83 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.008 0.001 TYR C 53 PHE 0.006 0.001 PHE A 464 TRP 0.006 0.001 TRP A 473 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 5517) covalent geometry : angle 0.45295 / 0.24 ( 7518) SS BOND : bond 0.00212 / 0.11 ( 3) SS BOND : angle 0.64846 / 0.31 ( 6) hydrogen bonds : bond 0.03586 / 2.44 ( 350) hydrogen bonds : angle 4.55520 / 3.30 ( 1014) ********************** 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 78 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6075 (tmm) cc_final: 0.5319 (mmt) REVERT: A 548 LYS cc_start: 0.7711 (mttt) cc_final: 0.6790 (mptt) REVERT: B 4 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6589 (mt) REVERT: B 99 ASN cc_start: 0.8009 (m-40) cc_final: 0.6943 (m-40) REVERT: C 74 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6386 (m-30) REVERT: C 109 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5430 (mt-10) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.1638 time to fit residues: 16.7111 Evaluate side-chains 75 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 109 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: 0.8980 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.162236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.132551 restraints weight = 15527.014| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.66 r_work: 0.3222 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5520 Z= 0.148 Angle : 0.480 4.837 7524 Z= 0.256 Chirality : 0.039 0.150 897 Planarity : 0.004 0.046 928 Dihedral : 4.648 48.939 746 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.03 % Allowed : 20.78 % Favored : 77.20 % 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: 1.64 (0.32), residues: 697 helix: 2.27 (0.27), residues: 368 sheet: 0.84 (0.51), residues: 111 loop : -0.88 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 18 TYR 0.010 0.001 TYR C 53 PHE 0.007 0.001 PHE B 95 TRP 0.009 0.001 TRP B 47 HIS 0.006 0.002 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 5517) covalent geometry : angle 0.47942 / 0.26 ( 7518) SS BOND : bond 0.00265 / 0.13 ( 3) SS BOND : angle 0.65345 / 0.30 ( 6) hydrogen bonds : bond 0.03945 / 2.70 ( 350) hydrogen bonds : angle 4.67984 / 3.39 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3096.04 seconds wall clock time: 53 minutes 8.09 seconds (3188.09 seconds total)