Starting phenix.real_space_refine on Thu Jul 2 02:13:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9shp_54907/07_2026/9shp_54907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9shp_54907/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9shp_54907/07_2026/9shp_54907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9shp_54907/07_2026/9shp_54907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9shp_54907/07_2026/9shp_54907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9shp_54907/07_2026/9shp_54907.map" } 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-dev-6108/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: 1.45, per 1000 atoms: 0.26 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: 0.48 Conformation dependent library (CDL) restraints added in 200.7 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: 0.18 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: 0.84 Time building geometry restraints manager: 0.64 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=" O5' C C 4 " pdb=" C5' C C 4 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.75e+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 ... (remaining 5675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 7615 1.95 - 3.91: 99 3.91 - 5.86: 22 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=" 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 1.50e+00 4.44e-01 1.52e+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=" 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 angle pdb=" OG1 THR B 771 " pdb=" CB THR B 771 " pdb=" CG2 THR B 771 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.95e+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: 883 0.118 - 0.235: 15 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: 1.010 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.510 ------------------------------------------------------------------------------- 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= 0.155 Angle : 0.618 9.764 7744 Z= 0.321 Chirality : 0.051 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 / 0.15 ( 5680) covalent geometry : angle 0.61848 / 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 : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0872 time to fit residues: 5.5899 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 : 0.215 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 HIS B 852 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.085058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.074501 restraints weight = 24830.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.076144 restraints weight = 14401.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.077342 restraints weight = 9775.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.078199 restraints weight = 7318.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.078760 restraints weight = 5847.391| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1078 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= 0.144 Angle : 0.604 6.808 7744 Z= 0.320 Chirality : 0.045 0.141 900 Planarity : 0.005 0.049 962 Dihedral : 9.271 73.190 845 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.74 % Allowed : 32.94 % 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: -2.07 (0.30), residues: 680 helix: -0.48 (0.36), residues: 190 sheet: -2.13 (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 218 TYR 0.007 0.001 TYR B 860 PHE 0.014 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 0.00310 / 0.14 ( 5680) covalent geometry : angle 0.60430 / 0.32 ( 7744) hydrogen bonds : bond 0.06601 / 4.44 ( 170) hydrogen bonds : angle 6.52834 / 4.78 ( 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 : 0.219 Fit side-chains revert: symmetry clash REVERT: B 622 MET cc_start: 0.6844 (ppp) cc_final: 0.6470 (pmm) outliers start: 22 outliers final: 8 residues processed: 60 average time/residue: 0.0770 time to fit residues: 6.2680 Evaluate side-chains 46 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 712 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: 0.2980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.0070 chunk 11 optimal weight: 3.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.084522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.073932 restraints weight = 25048.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.075528 restraints weight = 14790.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.076746 restraints weight = 10153.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.077415 restraints weight = 7651.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.078129 restraints weight = 6317.170| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5680 Z= 0.141 Angle : 0.589 10.204 7744 Z= 0.298 Chirality : 0.044 0.149 900 Planarity : 0.004 0.045 962 Dihedral : 8.929 73.110 839 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.07 % Allowed : 32.26 % 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: -2.16 (0.30), residues: 680 helix: -0.37 (0.37), residues: 191 sheet: -2.14 (0.41), residues: 146 loop : -1.68 (0.30), residues: 343 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 0.016 0.001 PHE B 470 TRP 0.009 0.001 TRP B 687 HIS 0.005 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 5680) covalent geometry : angle 0.58862 / 0.30 ( 7744) hydrogen bonds : bond 0.05435 / 3.68 ( 170) hydrogen bonds : angle 6.04191 / 4.40 ( 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 65 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: B 622 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6589 (pmm) REVERT: B 662 ARG cc_start: 0.6021 (OUTLIER) cc_final: 0.5437 (tpm170) REVERT: B 732 TYR cc_start: 0.3836 (OUTLIER) cc_final: 0.2558 (m-80) outliers start: 24 outliers final: 11 residues processed: 61 average time/residue: 0.0732 time to fit residues: 6.1332 Evaluate side-chains 49 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 258 LEU 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 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: 0.5980 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3772 r_free = 0.3772 target = 0.084410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073954 restraints weight = 24927.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.075609 restraints weight = 14419.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.076793 restraints weight = 9776.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.077661 restraints weight = 7331.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.078165 restraints weight = 5834.842| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1679 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= 0.120 Angle : 0.558 9.244 7744 Z= 0.284 Chirality : 0.044 0.134 900 Planarity : 0.004 0.042 962 Dihedral : 8.748 73.098 839 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.74 % Allowed : 33.28 % Favored : 62.99 % 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: -2.11 (0.30), residues: 680 helix: -0.26 (0.37), residues: 191 sheet: -2.18 (0.40), residues: 146 loop : -1.66 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.010 0.001 TYR B 575 PHE 0.015 0.001 PHE B 470 TRP 0.007 0.001 TRP B 687 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 5680) covalent geometry : angle 0.55796 / 0.28 ( 7744) hydrogen bonds : bond 0.04752 / 3.21 ( 170) hydrogen bonds : angle 5.71885 / 4.14 ( 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 60 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 404 MET cc_start: 0.7889 (tmm) cc_final: 0.7493 (tmm) REVERT: B 532 MET cc_start: 0.8319 (mmm) cc_final: 0.8038 (mmm) REVERT: B 622 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6687 (pmm) REVERT: B 662 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5541 (tpm170) REVERT: B 732 TYR cc_start: 0.3823 (OUTLIER) cc_final: 0.2577 (m-80) outliers start: 22 outliers final: 13 residues processed: 55 average time/residue: 0.0772 time to fit residues: 5.8115 Evaluate side-chains 52 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 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 179 VAL 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 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 662 ARG Chi-restraints excluded: chain B residue 694 MET 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: 9.9990 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.081414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070838 restraints weight = 26251.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.072437 restraints weight = 15356.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.073581 restraints weight = 10487.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.074383 restraints weight = 7965.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.074943 restraints weight = 6449.055| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5680 Z= 0.223 Angle : 0.624 9.968 7744 Z= 0.323 Chirality : 0.045 0.145 900 Planarity : 0.004 0.042 962 Dihedral : 8.825 73.496 839 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.26 % Allowed : 33.11 % 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: -2.45 (0.30), residues: 680 helix: -0.58 (0.37), residues: 199 sheet: -2.30 (0.40), residues: 146 loop : -1.91 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 504 TYR 0.016 0.002 TYR B 575 PHE 0.020 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 0.00503 / 0.22 ( 5680) covalent geometry : angle 0.62379 / 0.32 ( 7744) hydrogen bonds : bond 0.05059 / 3.39 ( 170) hydrogen bonds : angle 5.76843 / 4.20 ( 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 66 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 35 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8132 (pttp) cc_final: 0.7800 (tptm) REVERT: B 476 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5697 (m-80) REVERT: B 622 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6896 (pmm) REVERT: B 732 TYR cc_start: 0.4432 (OUTLIER) cc_final: 0.3166 (m-80) outliers start: 31 outliers final: 19 residues processed: 60 average time/residue: 0.0891 time to fit residues: 7.0143 Evaluate side-chains 55 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 33 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 218 ARG 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 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 630 VAL Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 overall best weight: 0.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.082244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.071624 restraints weight = 25753.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.073253 restraints weight = 15133.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.074452 restraints weight = 10315.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.075234 restraints weight = 7727.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.075875 restraints weight = 6248.514| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5680 Z= 0.142 Angle : 0.582 14.601 7744 Z= 0.291 Chirality : 0.044 0.176 900 Planarity : 0.004 0.041 962 Dihedral : 8.676 73.210 839 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.75 % Allowed : 33.28 % Favored : 61.97 % 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: -2.36 (0.30), residues: 680 helix: -0.48 (0.36), residues: 200 sheet: -2.31 (0.40), residues: 146 loop : -1.83 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 420 TYR 0.014 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 0.00317 / 0.14 ( 5680) covalent geometry : angle 0.58173 / 0.29 ( 7744) hydrogen bonds : bond 0.04462 / 2.99 ( 170) hydrogen bonds : angle 5.57890 / 4.03 ( 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 65 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 37 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8239 (pttp) cc_final: 0.7749 (tptp) REVERT: B 430 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8110 (t-90) REVERT: B 476 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5538 (m-80) REVERT: B 622 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6834 (pmm) REVERT: B 732 TYR cc_start: 0.3937 (OUTLIER) cc_final: 0.2652 (m-80) outliers start: 28 outliers final: 19 residues processed: 59 average time/residue: 0.0765 time to fit residues: 6.1841 Evaluate side-chains 59 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.082806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.072225 restraints weight = 25719.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.073859 restraints weight = 14958.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.075011 restraints weight = 10175.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.075855 restraints weight = 7695.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.076284 restraints weight = 6190.213| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5680 Z= 0.130 Angle : 0.587 14.358 7744 Z= 0.287 Chirality : 0.044 0.162 900 Planarity : 0.004 0.040 962 Dihedral : 8.571 73.179 839 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.60 % Allowed : 32.94 % Favored : 61.46 % 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: -0.30 (0.37), residues: 200 sheet: -2.15 (0.39), residues: 164 loop : -1.87 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 662 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 0.00292 / 0.13 ( 5680) covalent geometry : angle 0.58701 / 0.29 ( 7744) hydrogen bonds : bond 0.04152 / 2.79 ( 170) hydrogen bonds : angle 5.42542 / 3.89 ( 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 71 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 38 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: B 257 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8802 (tp) REVERT: B 430 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.8101 (t-90) REVERT: B 476 PHE cc_start: 0.6591 (OUTLIER) cc_final: 0.5708 (m-80) REVERT: B 622 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6917 (pmm) REVERT: B 732 TYR cc_start: 0.3902 (OUTLIER) cc_final: 0.2655 (m-80) outliers start: 33 outliers final: 21 residues processed: 65 average time/residue: 0.0693 time to fit residues: 6.2320 Evaluate side-chains 60 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 476 PHE 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 630 VAL Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.083020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.072472 restraints weight = 25727.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.074026 restraints weight = 15368.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.075164 restraints weight = 10610.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.075897 restraints weight = 8060.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.076542 restraints weight = 6601.372| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2330 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= 0.133 Angle : 0.590 14.564 7744 Z= 0.287 Chirality : 0.044 0.164 900 Planarity : 0.004 0.050 962 Dihedral : 8.542 73.179 839 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.92 % Allowed : 33.62 % Favored : 61.46 % 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: -2.18 (0.30), residues: 680 helix: -0.22 (0.37), residues: 201 sheet: -2.18 (0.40), residues: 150 loop : -1.82 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 218 TYR 0.014 0.001 TYR B 575 PHE 0.015 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 0.00300 / 0.13 ( 5680) covalent geometry : angle 0.59047 / 0.29 ( 7744) hydrogen bonds : bond 0.04039 / 2.71 ( 170) hydrogen bonds : angle 5.38197 / 3.85 ( 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 : 0.212 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8292 (pttp) cc_final: 0.7825 (tptp) REVERT: B 257 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8635 (tp) REVERT: B 430 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.7989 (t-90) REVERT: B 476 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.5724 (m-80) REVERT: B 622 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6962 (pmm) REVERT: B 732 TYR cc_start: 0.3882 (OUTLIER) cc_final: 0.2642 (m-80) outliers start: 29 outliers final: 21 residues processed: 59 average time/residue: 0.0579 time to fit residues: 4.9166 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 : 0.212 ------------------------------------------------------------------------------- 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 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 630 VAL Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET 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: 3.9990 chunk 14 optimal weight: 0.0000 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.082356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071896 restraints weight = 26086.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.073496 restraints weight = 15755.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074650 restraints weight = 10905.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075402 restraints weight = 8241.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.076007 restraints weight = 6715.679| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5680 Z= 0.164 Angle : 0.612 14.770 7744 Z= 0.299 Chirality : 0.044 0.160 900 Planarity : 0.004 0.040 962 Dihedral : 8.563 73.232 839 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.75 % Allowed : 33.28 % Favored : 61.97 % 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: -0.22 (0.37), residues: 201 sheet: -2.21 (0.38), residues: 164 loop : -1.89 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 218 TYR 0.015 0.001 TYR B 575 PHE 0.017 0.002 PHE B 470 TRP 0.006 0.001 TRP B 442 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 5680) covalent geometry : angle 0.61237 / 0.30 ( 7744) hydrogen bonds : bond 0.04147 / 2.78 ( 170) hydrogen bonds : angle 5.40757 / 3.87 ( 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 : 0.178 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8289 (pttp) cc_final: 0.7858 (mmtt) REVERT: B 257 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8671 (tp) REVERT: B 430 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8058 (t-90) REVERT: B 476 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.5743 (m-80) REVERT: B 523 MET cc_start: 0.7606 (pmm) cc_final: 0.7319 (pmm) REVERT: B 622 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7085 (pmm) REVERT: B 732 TYR cc_start: 0.3939 (OUTLIER) cc_final: 0.2675 (m-80) outliers start: 28 outliers final: 22 residues processed: 59 average time/residue: 0.0597 time to fit residues: 5.0660 Evaluate side-chains 61 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 636 HIS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET 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 28 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.083590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.073057 restraints weight = 25906.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074661 restraints weight = 15284.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.075820 restraints weight = 10518.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076640 restraints weight = 7905.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.077095 restraints weight = 6369.413| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5680 Z= 0.104 Angle : 0.593 14.823 7744 Z= 0.284 Chirality : 0.044 0.175 900 Planarity : 0.004 0.040 962 Dihedral : 8.484 73.173 839 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.41 % Allowed : 33.62 % Favored : 61.97 % 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: -2.06 (0.31), residues: 680 helix: -0.10 (0.37), residues: 201 sheet: -2.16 (0.41), residues: 145 loop : -1.74 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 218 TYR 0.013 0.001 TYR B 575 PHE 0.012 0.001 PHE B 470 TRP 0.010 0.001 TRP B 442 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 5680) covalent geometry : angle 0.59284 / 0.28 ( 7744) hydrogen bonds : bond 0.03766 / 2.52 ( 170) hydrogen bonds : angle 5.31100 / 3.78 ( 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 64 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 38 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8272 (pttp) cc_final: 0.7848 (mmtt) REVERT: B 257 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8605 (tp) REVERT: B 430 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7971 (t-90) REVERT: B 622 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6940 (pmm) REVERT: B 732 TYR cc_start: 0.3816 (OUTLIER) cc_final: 0.2614 (m-80) outliers start: 26 outliers final: 21 residues processed: 59 average time/residue: 0.0581 time to fit residues: 4.9850 Evaluate side-chains 61 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.083408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.073032 restraints weight = 25626.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.074647 restraints weight = 15261.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.075856 restraints weight = 10489.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.076617 restraints weight = 7881.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.077240 restraints weight = 6386.971| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2523 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= 0.117 Angle : 0.591 14.845 7744 Z= 0.285 Chirality : 0.044 0.165 900 Planarity : 0.004 0.040 962 Dihedral : 8.458 73.159 839 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.07 % Allowed : 34.47 % Favored : 61.46 % 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 (0.31), residues: 680 helix: -0.02 (0.38), residues: 201 sheet: -2.16 (0.40), residues: 152 loop : -1.80 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 218 TYR 0.011 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 0.00269 / 0.12 ( 5680) covalent geometry : angle 0.59121 / 0.28 ( 7744) hydrogen bonds : bond 0.03720 / 2.49 ( 170) hydrogen bonds : angle 5.25946 / 3.75 ( 465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 995.52 seconds wall clock time: 18 minutes 0.08 seconds (1080.08 seconds total)