Starting phenix.real_space_refine on Tue Aug 4 18:00:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9shp_54907/08_2026/9shp_54907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9shp_54907/08_2026/9shp_54907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9shp_54907/08_2026/9shp_54907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9shp_54907/08_2026/9shp_54907.map" model { file = "/net/cci-nas-00/data/ceres_data/9shp_54907/08_2026/9shp_54907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9shp_54907/08_2026/9shp_54907.cif" } resolution = 3.7 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= 0.013 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 6 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3529 2.51 5 N 960 2.21 5 O 1026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5554 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5428 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 657} Chain breaks: 4 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 154 Planarities with less than four sites: {'ARG:plan': 12, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.05, per 1000 atoms: 0.19 Number of scatterers: 5554 At special positions: 0 Unit cell: (72.8584, 76.9825, 118.223, 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 32 16.00 P 6 15.00 Mg 1 11.99 O 1026 8.00 N 960 7.00 C 3529 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: 0.47 Conformation dependent library (CDL) restraints added in 123.8 milliseconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1310 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 31.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 143 through 150 removed outlier: 3.507A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 208 through 223 removed outlier: 4.051A pdb=" N ASN B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 299 through 305 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.610A pdb=" N MET B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N HIS B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 3.938A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.630A pdb=" N ASP B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 518 removed outlier: 4.353A pdb=" N SER B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.784A pdb=" N MET B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.712A pdb=" N LEU B 546 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 579 removed outlier: 3.679A pdb=" N CYS B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.548A pdb=" N LEU B 607 " --> pdb=" O THR B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 691 removed outlier: 3.520A pdb=" N VAL B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG B 685 " --> pdb=" O GLN B 681 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 689 " --> pdb=" O ARG B 685 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS B 690 " --> pdb=" O ALA B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.600A pdb=" N VAL B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 805 through 816 removed outlier: 3.568A pdb=" N ILE B 809 " --> pdb=" O LYS B 805 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 810 " --> pdb=" O PRO B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 830 through 846 Processing sheet with id=AA1, first strand: chain 'B' and resid 452 through 456 Processing sheet with id=AA2, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.547A pdb=" N LEU B 266 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 265 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.560A pdb=" N THR B 123 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.597A pdb=" N THR B 197 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 192 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 184 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 229 removed outlier: 4.013A pdb=" N TRP B 250 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 273 " --> pdb=" O TRP B 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AA7, first strand: chain 'B' and resid 463 through 464 removed outlier: 3.675A pdb=" N ILE B 463 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 531 through 534 removed outlier: 3.700A pdb=" N ILE B 533 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 558 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 557 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL B 587 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N CYS B 559 " --> pdb=" O VAL B 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 659 through 664 removed outlier: 3.743A pdb=" N VAL B 649 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 631 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE B 629 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N MET B 628 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N TYR B 701 " --> pdb=" O MET B 628 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 630 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 738 " --> pdb=" O ILE B 798 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 465 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: 0.81 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1781 1.34 - 1.46: 1006 1.46 - 1.57: 2834 1.57 - 1.69: 11 1.69 - 1.81: 48 Bond restraints: 5680 Sorted by residual: bond pdb=" N LYS B 612 " pdb=" CA LYS B 612 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.29e+00 bond pdb=" P U C 1 " pdb=" OP3 U C 1 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" P C C 4 " pdb=" OP2 C C 4 " ideal model delta sigma weight residual 1.485 1.521 -0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" P U C 1 " pdb=" OP2 U C 1 " ideal model delta sigma weight residual 1.485 1.518 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" P C C 5 " pdb=" OP2 C C 5 " ideal model delta sigma weight residual 1.485 1.517 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 5675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 7607 1.95 - 3.91: 108 3.91 - 5.86: 21 5.86 - 7.81: 5 7.81 - 9.76: 3 Bond angle restraints: 7744 Sorted by residual: angle pdb=" C TYR B 861 " pdb=" N LEU B 862 " pdb=" CA LEU B 862 " ideal model delta sigma weight residual 121.70 128.79 -7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" CB MET B 284 " pdb=" CG MET B 284 " pdb=" SD MET B 284 " ideal model delta sigma weight residual 112.70 122.46 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" O5' U C 2 " pdb=" C5' U C 2 " pdb=" C4' U C 2 " ideal model delta sigma weight residual 109.40 111.90 -2.50 8.00e-01 1.56e+00 9.80e+00 angle pdb=" O3' C C 4 " pdb=" P C C 5 " pdb=" O5' C C 5 " ideal model delta sigma weight residual 104.00 98.14 5.86 1.90e+00 2.77e-01 9.50e+00 angle pdb=" CA PRO B 806 " pdb=" N PRO B 806 " pdb=" CD PRO B 806 " ideal model delta sigma weight residual 112.00 107.77 4.23 1.40e+00 5.10e-01 9.14e+00 ... (remaining 7739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 2842 16.95 - 33.91: 413 33.91 - 50.86: 138 50.86 - 67.82: 26 67.82 - 84.77: 8 Dihedral angle restraints: 3427 sinusoidal: 1401 harmonic: 2026 Sorted by residual: dihedral pdb=" CA TRP B 659 " pdb=" C TRP B 659 " pdb=" N PHE B 660 " pdb=" CA PHE B 660 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG B 147 " pdb=" CD ARG B 147 " pdb=" NE ARG B 147 " pdb=" CZ ARG B 147 " ideal model delta sinusoidal sigma weight residual 180.00 135.46 44.54 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU B 616 " pdb=" CG GLU B 616 " pdb=" CD GLU B 616 " pdb=" OE1 GLU B 616 " ideal model delta sinusoidal sigma weight residual 0.00 -84.77 84.77 1 3.00e+01 1.11e-03 9.69e+00 ... (remaining 3424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 880 0.118 - 0.235: 18 0.235 - 0.353: 0 0.353 - 0.471: 0 0.471 - 0.588: 2 Chirality restraints: 900 Sorted by residual: chirality pdb=" P U C 1 " pdb=" OP1 U C 1 " pdb=" OP2 U C 1 " pdb=" O5' U C 1 " both_signs ideal model delta sigma weight residual True 2.41 3.00 -0.59 2.00e-01 2.50e+01 8.66e+00 chirality pdb=" P C C 4 " pdb=" OP1 C C 4 " pdb=" OP2 C C 4 " pdb=" O5' C C 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CB THR B 771 " pdb=" CA THR B 771 " pdb=" OG1 THR B 771 " pdb=" CG2 THR B 771 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 897 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 805 " -0.063 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO B 806 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 806 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 806 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 622 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO B 623 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 623 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 623 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 125 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO B 126 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.021 5.00e-02 4.00e+02 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 37 2.50 - 3.10: 3867 3.10 - 3.70: 8252 3.70 - 4.30: 11240 4.30 - 4.90: 18504 Nonbonded interactions: 41900 Sorted by model distance: nonbonded pdb=" NE2 GLN B 608 " pdb="MG MG B 901 " model vdw 1.896 2.250 nonbonded pdb=" OE1 GLN B 585 " pdb="MG MG B 901 " model vdw 2.125 2.170 nonbonded pdb=" O ILE B 809 " pdb=" OG1 THR B 813 " model vdw 2.214 3.040 nonbonded pdb=" O LEU B 516 " pdb=" OG1 THR B 520 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN B 505 " pdb=" OG SER B 562 " model vdw 2.253 3.040 ... (remaining 41895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.670 Find NCS groups from input model: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.003 0.068 5680 Z= 0.158 Angle : 0.624 9.764 7744 Z= 0.325 Chirality : 0.052 0.588 900 Planarity : 0.005 0.094 962 Dihedral : 18.124 84.770 2117 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.51 % Allowed : 33.62 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.19 (0.31), residues: 680 helix: -0.53 (0.38), residues: 175 sheet: -2.24 (0.42), residues: 142 loop : -1.54 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 420 TYR 0.010 0.001 TYR B 776 PHE 0.016 0.002 PHE B 778 TRP 0.011 0.001 TRP B 442 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 5680) covalent geometry : angle 0.62412 / 0.32 ( 7744) hydrogen bonds : bond 0.29219 / 19.34 ( 170) hydrogen bonds : angle 9.41250 / 6.89 ( 465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0666 time to fit residues: 4.3424 Evaluate side-chains 39 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 HIS B 852 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.085074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.074482 restraints weight = 24951.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.076143 restraints weight = 14379.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.077377 restraints weight = 9736.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.078237 restraints weight = 7257.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.078723 restraints weight = 5781.294| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5680 Z= 0.143 Angle : 0.606 6.685 7744 Z= 0.320 Chirality : 0.045 0.143 900 Planarity : 0.005 0.048 962 Dihedral : 9.349 73.051 845 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.74 % Allowed : 32.60 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.08 (0.30), residues: 680 helix: -0.50 (0.36), residues: 190 sheet: -2.14 (0.44), residues: 127 loop : -1.54 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 420 TYR 0.009 0.001 TYR B 501 PHE 0.013 0.001 PHE B 470 TRP 0.012 0.001 TRP B 687 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 5680) covalent geometry : angle 0.60637 / 0.32 ( 7744) hydrogen bonds : bond 0.06295 / 4.22 ( 170) hydrogen bonds : angle 6.48414 / 4.74 ( 465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 622 MET cc_start: 0.6785 (ppp) cc_final: 0.6401 (pmm) outliers start: 22 outliers final: 7 residues processed: 60 average time/residue: 0.0629 time to fit residues: 5.1659 Evaluate side-chains 45 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 551 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.085532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.074999 restraints weight = 24766.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.076620 restraints weight = 14427.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.077853 restraints weight = 9848.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.078687 restraints weight = 7386.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.079215 restraints weight = 5932.407| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5680 Z= 0.116 Angle : 0.579 9.894 7744 Z= 0.291 Chirality : 0.044 0.149 900 Planarity : 0.004 0.044 962 Dihedral : 9.016 73.076 839 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.06 % Allowed : 33.62 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.09 (0.30), residues: 680 helix: -0.30 (0.36), residues: 190 sheet: -2.13 (0.42), residues: 132 loop : -1.67 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.010 0.001 TYR B 501 PHE 0.013 0.001 PHE B 470 TRP 0.009 0.001 TRP B 687 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 5680) covalent geometry : angle 0.57861 / 0.29 ( 7744) hydrogen bonds : bond 0.05370 / 3.65 ( 170) hydrogen bonds : angle 5.96126 / 4.33 ( 465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 622 MET cc_start: 0.6874 (ppp) cc_final: 0.6469 (pmm) REVERT: B 662 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5292 (tpm170) REVERT: B 732 TYR cc_start: 0.3723 (OUTLIER) cc_final: 0.2497 (m-80) outliers start: 18 outliers final: 9 residues processed: 57 average time/residue: 0.0535 time to fit residues: 4.2621 Evaluate side-chains 48 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 732 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.084352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.073833 restraints weight = 25378.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.075452 restraints weight = 14926.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.076664 restraints weight = 10240.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.077526 restraints weight = 7674.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.078008 restraints weight = 6135.918| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5680 Z= 0.131 Angle : 0.565 8.853 7744 Z= 0.287 Chirality : 0.044 0.168 900 Planarity : 0.004 0.041 962 Dihedral : 8.870 73.051 839 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.23 % Allowed : 33.62 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.30), residues: 680 helix: -0.24 (0.37), residues: 192 sheet: -2.13 (0.40), residues: 146 loop : -1.60 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 420 TYR 0.010 0.001 TYR B 575 PHE 0.016 0.001 PHE B 470 TRP 0.007 0.001 TRP B 687 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 5680) covalent geometry : angle 0.56464 / 0.29 ( 7744) hydrogen bonds : bond 0.04885 / 3.30 ( 170) hydrogen bonds : angle 5.78675 / 4.19 ( 465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: B 404 MET cc_start: 0.7874 (tmm) cc_final: 0.7514 (tmm) REVERT: B 532 MET cc_start: 0.8315 (mmm) cc_final: 0.8012 (mmm) REVERT: B 622 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6652 (pmm) REVERT: B 732 TYR cc_start: 0.3794 (OUTLIER) cc_final: 0.2541 (m-80) outliers start: 19 outliers final: 10 residues processed: 54 average time/residue: 0.0503 time to fit residues: 3.9292 Evaluate side-chains 46 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 732 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.081307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070683 restraints weight = 26349.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.072275 restraints weight = 15338.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.073421 restraints weight = 10507.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.074260 restraints weight = 7942.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.074781 restraints weight = 6391.673| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5680 Z= 0.249 Angle : 0.640 9.791 7744 Z= 0.332 Chirality : 0.046 0.144 900 Planarity : 0.005 0.042 962 Dihedral : 8.975 73.453 839 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.92 % Allowed : 33.28 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.30 (0.30), residues: 680 helix: -0.41 (0.37), residues: 193 sheet: -2.29 (0.40), residues: 146 loop : -1.79 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 504 TYR 0.015 0.002 TYR B 575 PHE 0.023 0.002 PHE B 470 TRP 0.009 0.002 TRP B 823 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 ( 5680) covalent geometry : angle 0.63995 / 0.33 ( 7744) hydrogen bonds : bond 0.05227 / 3.52 ( 170) hydrogen bonds : angle 5.82841 / 4.25 ( 465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 34 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 476 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5690 (m-80) REVERT: B 622 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6812 (pmm) REVERT: B 732 TYR cc_start: 0.4450 (OUTLIER) cc_final: 0.3183 (m-80) outliers start: 29 outliers final: 15 residues processed: 58 average time/residue: 0.0771 time to fit residues: 5.8192 Evaluate side-chains 51 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 33 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 56 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.082375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071821 restraints weight = 25755.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.073426 restraints weight = 15109.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.074651 restraints weight = 10325.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.075420 restraints weight = 7752.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.076033 restraints weight = 6286.854| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5680 Z= 0.145 Angle : 0.591 14.584 7744 Z= 0.297 Chirality : 0.044 0.182 900 Planarity : 0.004 0.040 962 Dihedral : 8.827 73.208 839 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.41 % Allowed : 33.28 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.41 (0.30), residues: 680 helix: -0.50 (0.36), residues: 200 sheet: -2.24 (0.39), residues: 160 loop : -1.89 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 662 TYR 0.013 0.001 TYR B 575 PHE 0.016 0.001 PHE B 470 TRP 0.007 0.001 TRP B 442 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 5680) covalent geometry : angle 0.59116 / 0.30 ( 7744) hydrogen bonds : bond 0.04591 / 3.07 ( 170) hydrogen bonds : angle 5.64278 / 4.07 ( 465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 35 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8188 (pttp) cc_final: 0.7605 (tptp) REVERT: B 430 HIS cc_start: 0.8583 (OUTLIER) cc_final: 0.8114 (t-90) REVERT: B 476 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.5580 (m-80) REVERT: B 622 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6798 (pmm) REVERT: B 732 TYR cc_start: 0.4349 (OUTLIER) cc_final: 0.3125 (m-80) outliers start: 26 outliers final: 19 residues processed: 56 average time/residue: 0.0694 time to fit residues: 5.3141 Evaluate side-chains 57 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 757 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 0.0010 chunk 33 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.083106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072451 restraints weight = 25971.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.074120 restraints weight = 15131.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.075283 restraints weight = 10297.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.076148 restraints weight = 7757.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.076744 restraints weight = 6237.136| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5680 Z= 0.119 Angle : 0.585 14.456 7744 Z= 0.284 Chirality : 0.044 0.162 900 Planarity : 0.004 0.039 962 Dihedral : 8.685 73.168 839 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.92 % Allowed : 33.45 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.30), residues: 680 helix: -0.29 (0.37), residues: 200 sheet: -2.13 (0.39), residues: 164 loop : -1.88 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 504 TYR 0.013 0.001 TYR B 575 PHE 0.014 0.001 PHE B 470 TRP 0.008 0.001 TRP B 442 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 5680) covalent geometry : angle 0.58500 / 0.28 ( 7744) hydrogen bonds : bond 0.04076 / 2.75 ( 170) hydrogen bonds : angle 5.39857 / 3.88 ( 465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8106 (pttp) cc_final: 0.7530 (tptp) REVERT: B 257 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8813 (tp) REVERT: B 430 HIS cc_start: 0.8583 (OUTLIER) cc_final: 0.8108 (t-90) REVERT: B 622 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6850 (pmm) REVERT: B 732 TYR cc_start: 0.3857 (OUTLIER) cc_final: 0.2622 (m-80) outliers start: 29 outliers final: 20 residues processed: 63 average time/residue: 0.0577 time to fit residues: 5.0744 Evaluate side-chains 60 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 36 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.081589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.071142 restraints weight = 25471.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.072730 restraints weight = 14904.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.073893 restraints weight = 10217.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.074553 restraints weight = 7707.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.075226 restraints weight = 6368.877| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5680 Z= 0.178 Angle : 0.610 14.594 7744 Z= 0.299 Chirality : 0.044 0.151 900 Planarity : 0.004 0.038 962 Dihedral : 8.738 73.306 839 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.92 % Allowed : 32.94 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.28 (0.30), residues: 680 helix: -0.25 (0.37), residues: 201 sheet: -2.18 (0.39), residues: 164 loop : -1.90 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 504 TYR 0.015 0.001 TYR B 575 PHE 0.017 0.002 PHE B 470 TRP 0.006 0.001 TRP B 823 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 5680) covalent geometry : angle 0.60975 / 0.30 ( 7744) hydrogen bonds : bond 0.04322 / 2.90 ( 170) hydrogen bonds : angle 5.41818 / 3.90 ( 465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 35 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8174 (pttp) cc_final: 0.7725 (tptp) REVERT: B 257 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8703 (tp) REVERT: B 430 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8121 (t-90) REVERT: B 476 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.5611 (m-80) REVERT: B 622 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6938 (pmm) REVERT: B 723 ASP cc_start: 0.8835 (m-30) cc_final: 0.8163 (p0) REVERT: B 732 TYR cc_start: 0.3950 (OUTLIER) cc_final: 0.2675 (m-80) outliers start: 29 outliers final: 20 residues processed: 60 average time/residue: 0.0655 time to fit residues: 5.5100 Evaluate side-chains 58 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 833 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.083064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.072531 restraints weight = 25877.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.074096 restraints weight = 15391.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.075224 restraints weight = 10601.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.076057 restraints weight = 8043.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076586 restraints weight = 6502.825| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5680 Z= 0.123 Angle : 0.595 14.872 7744 Z= 0.287 Chirality : 0.044 0.168 900 Planarity : 0.005 0.077 962 Dihedral : 8.685 73.199 839 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.75 % Allowed : 32.77 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.13 (0.31), residues: 680 helix: -0.18 (0.37), residues: 201 sheet: -2.07 (0.39), residues: 162 loop : -1.79 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 504 TYR 0.014 0.001 TYR B 575 PHE 0.014 0.001 PHE B 470 TRP 0.008 0.001 TRP B 442 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5680) covalent geometry : angle 0.59496 / 0.29 ( 7744) hydrogen bonds : bond 0.03995 / 2.68 ( 170) hydrogen bonds : angle 5.33492 / 3.82 ( 465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 36 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8194 (pttp) cc_final: 0.7736 (mmtt) REVERT: B 257 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8631 (tp) REVERT: B 430 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.8038 (t-90) REVERT: B 523 MET cc_start: 0.7574 (pmm) cc_final: 0.7299 (pmm) REVERT: B 622 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6864 (pmm) REVERT: B 723 ASP cc_start: 0.8680 (m-30) cc_final: 0.8122 (p0) REVERT: B 732 TYR cc_start: 0.3866 (OUTLIER) cc_final: 0.2637 (m-80) outliers start: 28 outliers final: 20 residues processed: 60 average time/residue: 0.0483 time to fit residues: 4.0411 Evaluate side-chains 58 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 833 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.083158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.072540 restraints weight = 26080.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.074138 restraints weight = 15577.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.075057 restraints weight = 10776.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.075989 restraints weight = 8405.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.076580 restraints weight = 6770.916| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5680 Z= 0.131 Angle : 0.592 14.956 7744 Z= 0.285 Chirality : 0.043 0.169 900 Planarity : 0.004 0.037 962 Dihedral : 8.587 73.237 839 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.24 % Allowed : 33.11 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.09 (0.31), residues: 680 helix: -0.13 (0.37), residues: 201 sheet: -2.06 (0.39), residues: 162 loop : -1.77 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 504 TYR 0.014 0.001 TYR B 575 PHE 0.015 0.001 PHE B 470 TRP 0.008 0.001 TRP B 442 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 5680) covalent geometry : angle 0.59232 / 0.29 ( 7744) hydrogen bonds : bond 0.03954 / 2.65 ( 170) hydrogen bonds : angle 5.31236 / 3.80 ( 465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8175 (pttp) cc_final: 0.7732 (mmtt) REVERT: B 257 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8618 (tp) REVERT: B 430 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8004 (t-90) REVERT: B 622 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6906 (pmm) REVERT: B 723 ASP cc_start: 0.8617 (m-30) cc_final: 0.8027 (p0) REVERT: B 732 TYR cc_start: 0.3863 (OUTLIER) cc_final: 0.2642 (m-80) outliers start: 25 outliers final: 21 residues processed: 54 average time/residue: 0.0517 time to fit residues: 4.0465 Evaluate side-chains 58 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 715 ASN Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.0050 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.083651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.073121 restraints weight = 25842.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.074688 restraints weight = 15337.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.075830 restraints weight = 10596.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.076563 restraints weight = 8034.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.077149 restraints weight = 6587.164| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5680 Z= 0.112 Angle : 0.582 15.138 7744 Z= 0.279 Chirality : 0.043 0.171 900 Planarity : 0.004 0.036 962 Dihedral : 8.482 73.212 839 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.41 % Allowed : 33.28 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.01 (0.31), residues: 680 helix: -0.05 (0.37), residues: 201 sheet: -2.00 (0.40), residues: 162 loop : -1.74 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 218 TYR 0.010 0.001 TYR B 575 PHE 0.013 0.001 PHE B 470 TRP 0.009 0.001 TRP B 442 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 5680) covalent geometry : angle 0.58185 / 0.28 ( 7744) hydrogen bonds : bond 0.03782 / 2.53 ( 170) hydrogen bonds : angle 5.25883 / 3.76 ( 465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 839.30 seconds wall clock time: 15 minutes 10.12 seconds (910.12 seconds total)