Starting phenix.real_space_refine on Thu Jul 2 05:15:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9i_64873/07_2026/9v9i_64873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9i_64873/07_2026/9v9i_64873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9i_64873/07_2026/9v9i_64873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9i_64873/07_2026/9v9i_64873.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9i_64873/07_2026/9v9i_64873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9i_64873/07_2026/9v9i_64873.cif" } resolution = 2.93 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= 0.035 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 P 33 5.49 5 Mg 2 5.21 5 S 15 5.16 5 C 4116 2.51 5 N 1219 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6716 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 6015 Classifications: {'peptide': 756} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 42, 'TRANS': 713} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.25 Number of scatterers: 6716 At special positions: 0 Unit cell: (79.143, 99.567, 101.269, 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 15 16.00 P 33 15.00 Mg 2 11.99 O 1331 8.00 N 1219 7.00 C 4116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 384.1 milliseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 32.0% alpha, 22.0% beta 4 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.755A pdb=" N ARG A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 131 removed outlier: 3.667A pdb=" N ALA A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.412A pdb=" N MET A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 removed outlier: 3.673A pdb=" N GLY A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 482 through 491 removed outlier: 3.806A pdb=" N LEU A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 516 through 531 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.594A pdb=" N PHE A 344 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.664A pdb=" N LEU A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 330 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.625A pdb=" N THR A 60 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 67 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 68 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 70 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 23 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A 99 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 25 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 239 removed outlier: 6.657A pdb=" N PHE A 274 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER A 235 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA A 272 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA8, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.987A pdb=" N LEU A 402 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN A 439 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 404 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP A 401 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 472 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL A 403 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 474 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 405 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 568 through 575 removed outlier: 3.543A pdb=" N ASP A 550 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE A 545 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N HIS A 615 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET A 547 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASP A 617 " --> pdb=" O MET A 547 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 549 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 649 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER A 679 " --> pdb=" O THR A 691 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1858 1.33 - 1.45: 1300 1.45 - 1.57: 3674 1.57 - 1.69: 64 1.69 - 1.81: 23 Bond restraints: 6919 Sorted by residual: bond pdb=" C GLU A 673 " pdb=" N ASN A 674 " ideal model delta sigma weight residual 1.330 1.416 -0.086 1.47e-02 4.63e+03 3.44e+01 bond pdb=" N MET A 311 " pdb=" CA MET A 311 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.18e-02 7.18e+03 7.85e+00 bond pdb=" N ASP A 408 " pdb=" CA ASP A 408 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.30e-02 5.92e+03 7.25e+00 bond pdb=" N SER A 109 " pdb=" CA SER A 109 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.34e-02 5.57e+03 5.84e+00 bond pdb=" N VAL A 308 " pdb=" CA VAL A 308 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.23e-02 6.61e+03 5.24e+00 ... (remaining 6914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 9155 1.64 - 3.28: 330 3.28 - 4.91: 47 4.91 - 6.55: 6 6.55 - 8.19: 3 Bond angle restraints: 9541 Sorted by residual: angle pdb=" O4' DG B 4 " pdb=" C4' DG B 4 " pdb=" C3' DG B 4 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT B 13 " pdb=" C4 DT B 13 " pdb=" O4 DT B 13 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B 1 " pdb=" C4 DT B 1 " pdb=" O4 DT B 1 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT B 16 " pdb=" C4 DT B 16 " pdb=" O4 DT B 16 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 9536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.99: 3917 27.99 - 55.97: 185 55.97 - 83.96: 21 83.96 - 111.95: 0 111.95 - 139.94: 1 Dihedral angle restraints: 4124 sinusoidal: 1944 harmonic: 2180 Sorted by residual: dihedral pdb=" C4' DG B 12 " pdb=" C3' DG B 12 " pdb=" O3' DG B 12 " pdb=" P DT B 13 " ideal model delta sinusoidal sigma weight residual 220.00 80.06 139.94 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA HIS A 206 " pdb=" C HIS A 206 " pdb=" N VAL A 207 " pdb=" CA VAL A 207 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TYR A 543 " pdb=" C TYR A 543 " pdb=" N ASP A 544 " pdb=" CA ASP A 544 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 843 0.047 - 0.095: 157 0.095 - 0.142: 61 0.142 - 0.189: 5 0.189 - 0.236: 1 Chirality restraints: 1067 Sorted by residual: chirality pdb=" CA GLN A 310 " pdb=" N GLN A 310 " pdb=" C GLN A 310 " pdb=" CB GLN A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA LEU A 405 " pdb=" N LEU A 405 " pdb=" C LEU A 405 " pdb=" CB LEU A 405 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA GLU A 634 " pdb=" N GLU A 634 " pdb=" C GLU A 634 " pdb=" CB GLU A 634 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1064 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 284 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 285 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 716 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 717 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 107 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C SER A 107 " -0.030 2.00e-02 2.50e+03 pdb=" O SER A 107 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 108 " 0.010 2.00e-02 2.50e+03 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 91 2.64 - 3.21: 5647 3.21 - 3.77: 9923 3.77 - 4.34: 14568 4.34 - 4.90: 23271 Nonbonded interactions: 53500 Sorted by model distance: nonbonded pdb=" OE1 GLN A 497 " pdb="MG MG A 801 " model vdw 2.080 2.170 nonbonded pdb=" OD2 ASP A 550 " pdb="MG MG A 802 " model vdw 2.120 2.170 nonbonded pdb=" OP2 DT B 1 " pdb="MG MG A 801 " model vdw 2.234 2.170 nonbonded pdb=" OD1 ASP A 550 " pdb="MG MG A 802 " model vdw 2.287 2.170 nonbonded pdb=" OH TYR A 546 " pdb=" OD2 ASP A 730 " model vdw 2.305 3.040 ... (remaining 53495 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 6919 Z= 0.267 Angle : 0.695 8.190 9541 Z= 0.439 Chirality : 0.044 0.236 1067 Planarity : 0.006 0.066 1133 Dihedral : 15.241 139.936 2720 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.47 % Allowed : 0.93 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.30), residues: 754 helix: 0.79 (0.36), residues: 218 sheet: -0.07 (0.38), residues: 202 loop : -0.05 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.014 0.002 TYR A 257 PHE 0.017 0.002 PHE A 159 TRP 0.010 0.001 TRP A 620 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.27 ( 6919) covalent geometry : angle 0.69458 / 0.44 ( 9541) hydrogen bonds : bond 0.21922 / 14.93 ( 260) hydrogen bonds : angle 8.16204 / 5.86 ( 736) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.179 Fit side-chains REVERT: A 484 TYR cc_start: 0.6933 (t80) cc_final: 0.6647 (t80) REVERT: A 654 LYS cc_start: 0.7451 (tptt) cc_final: 0.6812 (mttt) outliers start: 3 outliers final: 0 residues processed: 90 average time/residue: 0.6779 time to fit residues: 63.5904 Evaluate side-chains 56 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.190788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146431 restraints weight = 7635.822| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.02 r_work: 0.3427 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6919 Z= 0.132 Angle : 0.578 6.924 9541 Z= 0.313 Chirality : 0.042 0.154 1067 Planarity : 0.005 0.058 1133 Dihedral : 14.864 141.123 1256 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.56 % Allowed : 8.55 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.31), residues: 754 helix: 1.33 (0.36), residues: 224 sheet: 0.18 (0.39), residues: 198 loop : -0.17 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 490 TYR 0.013 0.001 TYR A 257 PHE 0.013 0.001 PHE A 245 TRP 0.013 0.001 TRP A 570 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 6919) covalent geometry : angle 0.57822 / 0.31 ( 9541) hydrogen bonds : bond 0.04903 / 3.37 ( 260) hydrogen bonds : angle 5.73092 / 4.24 ( 736) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.224 Fit side-chains REVERT: A 27 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6052 (tmm-80) REVERT: A 255 ARG cc_start: 0.6632 (ttt-90) cc_final: 0.6070 (tpt-90) REVERT: A 318 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 349 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7395 (tpt170) REVERT: A 484 TYR cc_start: 0.6951 (t80) cc_final: 0.6431 (t80) REVERT: A 485 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7199 (m-30) REVERT: A 654 LYS cc_start: 0.7337 (tptt) cc_final: 0.6633 (mttt) outliers start: 10 outliers final: 2 residues processed: 70 average time/residue: 0.5833 time to fit residues: 42.7965 Evaluate side-chains 61 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 485 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 ASN A 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.191990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147211 restraints weight = 7555.932| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.92 r_work: 0.3403 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6919 Z= 0.147 Angle : 0.557 6.923 9541 Z= 0.299 Chirality : 0.043 0.168 1067 Planarity : 0.005 0.050 1133 Dihedral : 14.896 140.125 1256 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.18 % Allowed : 9.64 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.31), residues: 754 helix: 1.42 (0.35), residues: 224 sheet: 0.01 (0.40), residues: 188 loop : -0.22 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.012 0.002 TYR A 380 PHE 0.012 0.001 PHE A 232 TRP 0.012 0.001 TRP A 570 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 6919) covalent geometry : angle 0.55695 / 0.30 ( 9541) hydrogen bonds : bond 0.04528 / 3.09 ( 260) hydrogen bonds : angle 5.24035 / 3.84 ( 736) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.231 Fit side-chains REVERT: A 27 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6100 (tmm-80) REVERT: A 255 ARG cc_start: 0.6881 (ttt-90) cc_final: 0.6465 (tpt-90) REVERT: A 484 TYR cc_start: 0.6993 (t80) cc_final: 0.6652 (t80) REVERT: A 485 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: A 654 LYS cc_start: 0.7371 (tptt) cc_final: 0.6686 (mttt) REVERT: A 665 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7513 (mt) outliers start: 14 outliers final: 4 residues processed: 68 average time/residue: 0.5889 time to fit residues: 42.1097 Evaluate side-chains 61 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.0000 chunk 45 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.192735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148105 restraints weight = 7632.025| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.94 r_work: 0.3412 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6919 Z= 0.130 Angle : 0.530 6.963 9541 Z= 0.286 Chirality : 0.042 0.155 1067 Planarity : 0.005 0.040 1133 Dihedral : 14.844 140.235 1256 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.56 % Allowed : 12.60 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.31), residues: 754 helix: 1.61 (0.35), residues: 224 sheet: 0.01 (0.40), residues: 188 loop : -0.19 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 490 TYR 0.012 0.001 TYR A 380 PHE 0.011 0.001 PHE A 232 TRP 0.012 0.001 TRP A 570 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6919) covalent geometry : angle 0.53013 / 0.29 ( 9541) hydrogen bonds : bond 0.03841 / 2.62 ( 260) hydrogen bonds : angle 5.01837 / 3.68 ( 736) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.182 Fit side-chains REVERT: A 27 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6105 (tmm-80) REVERT: A 255 ARG cc_start: 0.6892 (ttt-90) cc_final: 0.6494 (tpt-90) REVERT: A 435 ARG cc_start: 0.6546 (mmm-85) cc_final: 0.6310 (mmm-85) REVERT: A 484 TYR cc_start: 0.7004 (t80) cc_final: 0.6676 (t80) REVERT: A 485 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: A 654 LYS cc_start: 0.7331 (tptt) cc_final: 0.6654 (mttt) REVERT: A 665 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7496 (mt) REVERT: A 758 ARG cc_start: 0.6684 (mmm160) cc_final: 0.5667 (mmt90) outliers start: 10 outliers final: 2 residues processed: 63 average time/residue: 0.7540 time to fit residues: 49.6726 Evaluate side-chains 60 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 0.0000 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.191638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148415 restraints weight = 7652.085| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.07 r_work: 0.3392 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6919 Z= 0.154 Angle : 0.547 6.908 9541 Z= 0.293 Chirality : 0.042 0.162 1067 Planarity : 0.005 0.041 1133 Dihedral : 14.880 140.388 1256 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.02 % Allowed : 13.53 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.31), residues: 754 helix: 1.59 (0.35), residues: 225 sheet: -0.01 (0.40), residues: 188 loop : -0.18 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.012 0.001 TYR A 143 PHE 0.012 0.001 PHE A 232 TRP 0.012 0.001 TRP A 136 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 6919) covalent geometry : angle 0.54699 / 0.29 ( 9541) hydrogen bonds : bond 0.04047 / 2.74 ( 260) hydrogen bonds : angle 4.95258 / 3.61 ( 736) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6101 (tmm-80) REVERT: A 189 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7393 (m90) REVERT: A 255 ARG cc_start: 0.7004 (ttt-90) cc_final: 0.6567 (tpt-90) REVERT: A 484 TYR cc_start: 0.6947 (t80) cc_final: 0.6620 (t80) REVERT: A 485 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: A 654 LYS cc_start: 0.7373 (tptt) cc_final: 0.6705 (mttt) REVERT: A 665 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7538 (mt) REVERT: A 674 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8818 (m-40) REVERT: A 758 ARG cc_start: 0.6737 (mmm160) cc_final: 0.5700 (mmt90) outliers start: 13 outliers final: 3 residues processed: 64 average time/residue: 0.6806 time to fit residues: 45.6730 Evaluate side-chains 60 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 674 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.193641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148758 restraints weight = 7631.762| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.95 r_work: 0.3444 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6919 Z= 0.137 Angle : 0.525 6.935 9541 Z= 0.282 Chirality : 0.041 0.157 1067 Planarity : 0.005 0.073 1133 Dihedral : 14.860 140.566 1256 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.71 % Allowed : 14.93 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.31), residues: 754 helix: 1.69 (0.35), residues: 225 sheet: -0.05 (0.39), residues: 196 loop : -0.15 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.012 0.001 TYR A 380 PHE 0.011 0.001 PHE A 232 TRP 0.012 0.001 TRP A 65 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 6919) covalent geometry : angle 0.52452 / 0.28 ( 9541) hydrogen bonds : bond 0.03778 / 2.55 ( 260) hydrogen bonds : angle 4.83576 / 3.53 ( 736) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6110 (tmm-80) REVERT: A 189 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7399 (m90) REVERT: A 193 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 255 ARG cc_start: 0.6950 (ttt-90) cc_final: 0.6649 (tpt-90) REVERT: A 318 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: A 484 TYR cc_start: 0.6942 (t80) cc_final: 0.6671 (t80) REVERT: A 654 LYS cc_start: 0.7368 (tptt) cc_final: 0.6666 (mptt) REVERT: A 665 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7500 (mt) REVERT: A 758 ARG cc_start: 0.6696 (mmm160) cc_final: 0.5680 (mmt90) outliers start: 11 outliers final: 2 residues processed: 65 average time/residue: 0.6914 time to fit residues: 46.9825 Evaluate side-chains 62 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.0010 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.191576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147190 restraints weight = 7646.987| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.04 r_work: 0.3440 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6919 Z= 0.122 Angle : 0.514 6.943 9541 Z= 0.277 Chirality : 0.041 0.154 1067 Planarity : 0.005 0.063 1133 Dihedral : 14.839 140.634 1256 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.56 % Allowed : 15.71 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.31), residues: 754 helix: 1.79 (0.35), residues: 225 sheet: -0.03 (0.39), residues: 196 loop : -0.14 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 489 TYR 0.012 0.001 TYR A 380 PHE 0.010 0.001 PHE A 232 TRP 0.012 0.001 TRP A 570 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6919) covalent geometry : angle 0.51361 / 0.28 ( 9541) hydrogen bonds : bond 0.03579 / 2.41 ( 260) hydrogen bonds : angle 4.76591 / 3.48 ( 736) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6080 (tmm-80) REVERT: A 189 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7413 (m90) REVERT: A 193 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 255 ARG cc_start: 0.7021 (ttt-90) cc_final: 0.6595 (tpt-90) REVERT: A 318 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: A 387 MET cc_start: 0.8091 (mmp) cc_final: 0.7827 (mmm) REVERT: A 484 TYR cc_start: 0.6941 (t80) cc_final: 0.6641 (t80) REVERT: A 489 ARG cc_start: 0.6789 (ttm-80) cc_final: 0.6284 (mpt180) REVERT: A 654 LYS cc_start: 0.7249 (tptt) cc_final: 0.6591 (mptt) REVERT: A 665 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7490 (mt) REVERT: A 758 ARG cc_start: 0.6702 (mmm160) cc_final: 0.5691 (mmt90) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 0.5804 time to fit residues: 41.2843 Evaluate side-chains 64 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 4 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.190331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145294 restraints weight = 7688.050| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.97 r_work: 0.3385 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6919 Z= 0.169 Angle : 0.554 6.876 9541 Z= 0.297 Chirality : 0.042 0.163 1067 Planarity : 0.005 0.060 1133 Dihedral : 14.903 140.668 1256 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.02 % Allowed : 15.40 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.31), residues: 754 helix: 1.72 (0.35), residues: 225 sheet: -0.08 (0.39), residues: 196 loop : -0.21 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 435 TYR 0.013 0.002 TYR A 143 PHE 0.012 0.001 PHE A 323 TRP 0.016 0.002 TRP A 136 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 6919) covalent geometry : angle 0.55430 / 0.30 ( 9541) hydrogen bonds : bond 0.04026 / 2.71 ( 260) hydrogen bonds : angle 4.81570 / 3.51 ( 736) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6115 (tmm-80) REVERT: A 189 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7539 (m90) REVERT: A 193 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 255 ARG cc_start: 0.7023 (ttt-90) cc_final: 0.6717 (tpt-90) REVERT: A 318 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: A 484 TYR cc_start: 0.6948 (t80) cc_final: 0.6710 (t80) REVERT: A 654 LYS cc_start: 0.7307 (tptt) cc_final: 0.6630 (mptt) REVERT: A 665 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7524 (mt) REVERT: A 758 ARG cc_start: 0.6718 (mmm160) cc_final: 0.5705 (mmt90) outliers start: 13 outliers final: 3 residues processed: 68 average time/residue: 0.6368 time to fit residues: 45.4189 Evaluate side-chains 64 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.194335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150744 restraints weight = 7615.634| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.99 r_work: 0.3430 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6919 Z= 0.123 Angle : 0.515 6.919 9541 Z= 0.279 Chirality : 0.041 0.154 1067 Planarity : 0.005 0.056 1133 Dihedral : 14.827 140.871 1256 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.56 % Allowed : 16.33 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.31), residues: 754 helix: 1.81 (0.35), residues: 225 sheet: -0.01 (0.39), residues: 196 loop : -0.19 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.012 0.001 TYR A 380 PHE 0.010 0.001 PHE A 232 TRP 0.014 0.001 TRP A 136 HIS 0.002 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6919) covalent geometry : angle 0.51502 / 0.28 ( 9541) hydrogen bonds : bond 0.03546 / 2.38 ( 260) hydrogen bonds : angle 4.72601 / 3.45 ( 736) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6152 (tmm-80) REVERT: A 189 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7520 (m90) REVERT: A 193 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 255 ARG cc_start: 0.7008 (ttt-90) cc_final: 0.6749 (tpt-90) REVERT: A 318 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 387 MET cc_start: 0.8081 (mmp) cc_final: 0.7838 (mmm) REVERT: A 484 TYR cc_start: 0.7019 (t80) cc_final: 0.6688 (t80) REVERT: A 654 LYS cc_start: 0.7235 (tptt) cc_final: 0.6593 (mptt) REVERT: A 665 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7494 (mt) REVERT: A 758 ARG cc_start: 0.6713 (mmm160) cc_final: 0.5713 (mmt90) outliers start: 10 outliers final: 3 residues processed: 67 average time/residue: 0.6326 time to fit residues: 44.2933 Evaluate side-chains 62 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.191885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147314 restraints weight = 7697.619| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.06 r_work: 0.3422 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6919 Z= 0.148 Angle : 0.542 6.880 9541 Z= 0.291 Chirality : 0.042 0.160 1067 Planarity : 0.005 0.057 1133 Dihedral : 14.808 140.681 1256 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.40 % Allowed : 17.26 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.31), residues: 754 helix: 1.75 (0.35), residues: 225 sheet: 0.01 (0.40), residues: 196 loop : -0.26 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 489 TYR 0.013 0.001 TYR A 143 PHE 0.011 0.001 PHE A 323 TRP 0.013 0.001 TRP A 136 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6919) covalent geometry : angle 0.54244 / 0.29 ( 9541) hydrogen bonds : bond 0.03836 / 2.58 ( 260) hydrogen bonds : angle 4.73858 / 3.45 ( 736) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6139 (tmm-80) REVERT: A 189 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7560 (m90) REVERT: A 255 ARG cc_start: 0.7027 (ttt-90) cc_final: 0.6603 (tpt-90) REVERT: A 318 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 387 MET cc_start: 0.8140 (mmp) cc_final: 0.7893 (mmm) REVERT: A 484 TYR cc_start: 0.7011 (t80) cc_final: 0.6729 (t80) REVERT: A 654 LYS cc_start: 0.7270 (tptt) cc_final: 0.6616 (mptt) REVERT: A 665 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7517 (mt) REVERT: A 758 ARG cc_start: 0.6739 (mmm160) cc_final: 0.5732 (mmt90) outliers start: 9 outliers final: 2 residues processed: 66 average time/residue: 0.6258 time to fit residues: 43.3569 Evaluate side-chains 65 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 665 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.195170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150300 restraints weight = 7599.254| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.96 r_work: 0.3426 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6919 Z= 0.117 Angle : 0.521 7.406 9541 Z= 0.280 Chirality : 0.040 0.153 1067 Planarity : 0.005 0.055 1133 Dihedral : 14.717 140.809 1256 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.93 % Allowed : 17.88 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.31), residues: 754 helix: 1.87 (0.35), residues: 225 sheet: 0.12 (0.40), residues: 197 loop : -0.23 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 489 TYR 0.013 0.001 TYR A 380 PHE 0.009 0.001 PHE A 232 TRP 0.014 0.001 TRP A 136 HIS 0.002 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 6919) covalent geometry : angle 0.52058 / 0.28 ( 9541) hydrogen bonds : bond 0.03449 / 2.31 ( 260) hydrogen bonds : angle 4.65012 / 3.40 ( 736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.17 seconds wall clock time: 39 minutes 55.84 seconds (2395.84 seconds total)