Starting phenix.real_space_refine on Tue Feb 3 18:06:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s0z_54428/02_2026/9s0z_54428.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s0z_54428/02_2026/9s0z_54428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s0z_54428/02_2026/9s0z_54428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s0z_54428/02_2026/9s0z_54428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s0z_54428/02_2026/9s0z_54428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s0z_54428/02_2026/9s0z_54428.map" } resolution = 3.0 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= 0.019 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 5 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3680 2.51 5 N 1014 2.21 5 O 1063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5795 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5691 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 671} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} 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: 1.07, per 1000 atoms: 0.18 Number of scatterers: 5795 At special positions: 0 Unit cell: (79.056, 92.232, 111.264, 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 5 15.00 Mg 1 11.99 O 1063 8.00 N 1014 7.00 C 3680 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: 0.46 Conformation dependent library (CDL) restraints added in 126.3 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1336 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 34.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 299 through 306 removed outlier: 4.039A pdb=" N GLY B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 414 through 432 removed outlier: 4.021A pdb=" N LEU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 Processing helix chain 'B' and resid 505 through 524 removed outlier: 3.509A pdb=" N ILE B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.529A pdb=" N GLN B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 579 removed outlier: 3.683A pdb=" N TYR B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.713A pdb=" N GLY B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 691 removed outlier: 3.666A pdb=" N GLN B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 716 removed outlier: 3.795A pdb=" N LEU B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 727 removed outlier: 3.532A pdb=" N ASP B 723 " --> pdb=" O PRO B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 816 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 helix chain 'B' and resid 852 through 856 removed outlier: 3.691A pdb=" N LEU B 855 " --> pdb=" O ASN B 852 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 659 through 664 removed outlier: 3.669A pdb=" N ASP B 633 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE B 629 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N CYS B 634 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 698 " --> pdb=" O THR B 737 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE B 739 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 700 " --> pdb=" O ILE B 739 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL B 741 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG B 702 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU B 736 " --> pdb=" O ASP B 800 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP B 800 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 738 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS B 114 " --> pdb=" O GLN B 752 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 752 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 257 through 259 removed outlier: 5.224A pdb=" N ILE B 264 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 138 removed outlier: 5.524A pdb=" N LEU B 198 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N HIS B 134 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 200 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AA7, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.596A pdb=" N VAL B 309 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 308 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464 removed outlier: 3.628A pdb=" N ILE B 463 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 531 through 535 removed outlier: 6.283A pdb=" N LEU B 499 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 535 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR B 501 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 502 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 557 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 587 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N CYS B 559 " --> pdb=" O VAL B 587 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 678 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: 0.68 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1672 1.33 - 1.45: 926 1.45 - 1.57: 3273 1.57 - 1.69: 9 1.69 - 1.81: 48 Bond restraints: 5928 Sorted by residual: bond pdb=" O5' A C 3 " pdb=" C5' A C 3 " ideal model delta sigma weight residual 1.420 1.453 -0.033 1.50e-02 4.44e+03 4.95e+00 bond pdb=" P A C 3 " pdb=" OP2 A C 3 " ideal model delta sigma weight residual 1.485 1.517 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" P A C 3 " pdb=" O5' A C 3 " ideal model delta sigma weight residual 1.593 1.615 -0.022 1.50e-02 4.44e+03 2.16e+00 bond pdb=" CG1 ILE B 827 " pdb=" CD1 ILE B 827 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.42e+00 bond pdb=" C1' A C 3 " pdb=" N9 A C 3 " ideal model delta sigma weight residual 1.475 1.457 0.018 1.50e-02 4.44e+03 1.37e+00 ... (remaining 5923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 7845 1.59 - 3.19: 176 3.19 - 4.78: 27 4.78 - 6.38: 5 6.38 - 7.97: 5 Bond angle restraints: 8058 Sorted by residual: angle pdb=" C SER B 237 " pdb=" N ASP B 238 " pdb=" CA ASP B 238 " ideal model delta sigma weight residual 123.46 119.93 3.53 1.35e+00 5.49e-01 6.82e+00 angle pdb=" O2' A C 3 " pdb=" C2' A C 3 " pdb=" C1' A C 3 " ideal model delta sigma weight residual 108.40 112.01 -3.61 1.50e+00 4.44e-01 5.81e+00 angle pdb=" O3' U C 2 " pdb=" P A C 3 " pdb=" OP2 A C 3 " ideal model delta sigma weight residual 108.00 115.19 -7.19 3.00e+00 1.11e-01 5.75e+00 angle pdb=" CA LEU B 363 " pdb=" CB LEU B 363 " pdb=" CG LEU B 363 " ideal model delta sigma weight residual 116.30 124.27 -7.97 3.50e+00 8.16e-02 5.18e+00 angle pdb=" C ILE B 384 " pdb=" CA ILE B 384 " pdb=" CB ILE B 384 " ideal model delta sigma weight residual 110.89 113.20 -2.31 1.08e+00 8.57e-01 4.59e+00 ... (remaining 8053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.42: 3227 18.42 - 36.83: 282 36.83 - 55.25: 49 55.25 - 73.67: 9 73.67 - 92.08: 12 Dihedral angle restraints: 3579 sinusoidal: 1510 harmonic: 2069 Sorted by residual: dihedral pdb=" CA ASP B 433 " pdb=" CB ASP B 433 " pdb=" CG ASP B 433 " pdb=" OD1 ASP B 433 " ideal model delta sinusoidal sigma weight residual -30.00 -86.05 56.05 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA GLU B 654 " pdb=" C GLU B 654 " pdb=" N GLY B 655 " pdb=" CA GLY B 655 " ideal model delta harmonic sigma weight residual -180.00 -164.30 -15.70 0 5.00e+00 4.00e-02 9.86e+00 dihedral pdb=" CA GLN B 720 " pdb=" C GLN B 720 " pdb=" N PHE B 721 " pdb=" CA PHE B 721 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 ... (remaining 3576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 821 0.080 - 0.161: 85 0.161 - 0.241: 1 0.241 - 0.322: 1 0.322 - 0.402: 1 Chirality restraints: 909 Sorted by residual: chirality pdb=" P A C 3 " pdb=" OP1 A C 3 " pdb=" OP2 A C 3 " pdb=" O5' A C 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.81 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB ILE B 457 " pdb=" CA ILE B 457 " pdb=" CG1 ILE B 457 " pdb=" CG2 ILE B 457 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C2' A C 3 " pdb=" C3' A C 3 " pdb=" O2' A C 3 " pdb=" C1' A C 3 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 906 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 497 " -0.007 2.00e-02 2.50e+03 9.19e-03 2.11e+00 pdb=" CG TRP B 497 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 497 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 497 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 497 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 497 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 497 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 497 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 497 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 497 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 705 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C VAL B 705 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL B 705 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY B 706 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 829 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.72e+00 pdb=" N PRO B 830 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 830 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 830 " -0.018 5.00e-02 4.00e+02 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 35 2.50 - 3.10: 4070 3.10 - 3.70: 8806 3.70 - 4.30: 12655 4.30 - 4.90: 21229 Nonbonded interactions: 46795 Sorted by model distance: nonbonded pdb=" NE2 GLN B 608 " pdb="MG MG B 901 " model vdw 1.895 2.250 nonbonded pdb=" OP1 U C 1 " pdb="MG MG B 901 " model vdw 2.111 2.170 nonbonded pdb=" OE1 GLN B 608 " pdb="MG MG B 901 " model vdw 2.173 2.170 nonbonded pdb=" OXT LEU B 862 " pdb="MG MG B 901 " model vdw 2.219 2.170 nonbonded pdb=" NZ LYS B 566 " pdb=" O GLN B 845 " model vdw 2.222 3.120 ... (remaining 46790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.780 Find NCS groups from input model: 0.010 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:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 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 : 0.005 0.046 5928 Z= 0.205 Angle : 0.618 7.969 8058 Z= 0.319 Chirality : 0.049 0.402 909 Planarity : 0.004 0.033 1009 Dihedral : 15.051 92.082 2243 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.46 (0.31), residues: 692 helix: -0.72 (0.33), residues: 228 sheet: -0.81 (0.40), residues: 173 loop : -1.09 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 772 TYR 0.016 0.002 TYR B 313 PHE 0.019 0.002 PHE B 470 TRP 0.024 0.002 TRP B 497 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 5928) covalent geometry : angle 0.61792 ( 8058) hydrogen bonds : bond 0.25702 ( 238) hydrogen bonds : angle 9.21969 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.167 Fit side-chains REVERT: B 113 VAL cc_start: 0.7389 (p) cc_final: 0.7020 (t) REVERT: B 265 MET cc_start: 0.7071 (mtt) cc_final: 0.6779 (mtm) REVERT: B 476 PHE cc_start: 0.7092 (m-10) cc_final: 0.6768 (m-80) REVERT: B 494 LEU cc_start: 0.5102 (tp) cc_final: 0.4770 (tp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.5064 time to fit residues: 68.0988 Evaluate side-chains 52 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN B 225 ASN B 475 GLN B 510 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.111810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.092056 restraints weight = 14315.386| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.00 r_work: 0.3517 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5928 Z= 0.191 Angle : 0.709 8.941 8058 Z= 0.365 Chirality : 0.049 0.172 909 Planarity : 0.005 0.056 1009 Dihedral : 9.201 96.269 854 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.69 % Allowed : 14.10 % Favored : 83.20 % 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: -1.18 (0.30), residues: 692 helix: -0.01 (0.32), residues: 227 sheet: -0.78 (0.39), residues: 175 loop : -1.28 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 160 TYR 0.016 0.002 TYR B 776 PHE 0.020 0.002 PHE B 285 TRP 0.018 0.002 TRP B 497 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 5928) covalent geometry : angle 0.70889 ( 8058) hydrogen bonds : bond 0.04586 ( 238) hydrogen bonds : angle 6.48347 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 111 ILE cc_start: 0.7572 (mt) cc_final: 0.7345 (mm) REVERT: B 284 MET cc_start: 0.8365 (mtt) cc_final: 0.7788 (tmm) REVERT: B 397 MET cc_start: 0.3117 (ptp) cc_final: 0.2588 (ptp) REVERT: B 476 PHE cc_start: 0.7637 (m-10) cc_final: 0.7370 (m-80) outliers start: 17 outliers final: 5 residues processed: 73 average time/residue: 0.3531 time to fit residues: 27.4369 Evaluate side-chains 51 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.104186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.083795 restraints weight = 14197.489| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.06 r_work: 0.3373 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 5928 Z= 0.209 Angle : 0.666 12.676 8058 Z= 0.341 Chirality : 0.048 0.192 909 Planarity : 0.004 0.041 1009 Dihedral : 9.071 89.938 854 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.17 % Allowed : 17.75 % Favored : 79.08 % 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: -1.18 (0.30), residues: 692 helix: 0.24 (0.32), residues: 236 sheet: -1.13 (0.39), residues: 159 loop : -1.31 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 160 TYR 0.017 0.002 TYR B 542 PHE 0.032 0.002 PHE B 285 TRP 0.011 0.002 TRP B 325 HIS 0.006 0.002 HIS B 794 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 5928) covalent geometry : angle 0.66600 ( 8058) hydrogen bonds : bond 0.04481 ( 238) hydrogen bonds : angle 5.89925 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: B 111 ILE cc_start: 0.7859 (mt) cc_final: 0.7652 (mm) REVERT: B 161 CYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7142 (m) REVERT: B 231 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6484 (mtt-85) REVERT: B 323 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7939 (tp) REVERT: B 397 MET cc_start: 0.3380 (ptp) cc_final: 0.2782 (ptp) REVERT: B 462 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8368 (mmpt) outliers start: 20 outliers final: 4 residues processed: 65 average time/residue: 0.3076 time to fit residues: 21.3955 Evaluate side-chains 45 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.108547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.088207 restraints weight = 14401.908| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.91 r_work: 0.3489 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5928 Z= 0.141 Angle : 0.585 11.825 8058 Z= 0.294 Chirality : 0.045 0.163 909 Planarity : 0.004 0.045 1009 Dihedral : 8.796 91.028 854 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.85 % Allowed : 20.13 % Favored : 77.02 % 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: -0.90 (0.31), residues: 692 helix: 0.76 (0.33), residues: 230 sheet: -1.18 (0.40), residues: 156 loop : -1.26 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 484 TYR 0.013 0.001 TYR B 542 PHE 0.025 0.002 PHE B 285 TRP 0.008 0.001 TRP B 687 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5928) covalent geometry : angle 0.58465 ( 8058) hydrogen bonds : bond 0.03446 ( 238) hydrogen bonds : angle 5.45548 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 161 CYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6973 (m) REVERT: B 266 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8085 (tp) REVERT: B 284 MET cc_start: 0.7806 (mtt) cc_final: 0.7319 (tmm) REVERT: B 397 MET cc_start: 0.3763 (ptp) cc_final: 0.3220 (ptp) REVERT: B 462 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8479 (mmpt) REVERT: B 622 MET cc_start: 0.7406 (mmm) cc_final: 0.6549 (mmm) outliers start: 18 outliers final: 8 residues processed: 54 average time/residue: 0.4122 time to fit residues: 23.9239 Evaluate side-chains 43 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 468 LYS Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN B 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.106778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.087422 restraints weight = 14467.953| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.80 r_work: 0.3477 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5928 Z= 0.142 Angle : 0.586 11.666 8058 Z= 0.291 Chirality : 0.045 0.159 909 Planarity : 0.004 0.042 1009 Dihedral : 8.740 89.131 854 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.44 % Allowed : 20.13 % Favored : 75.44 % 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: -0.81 (0.31), residues: 692 helix: 1.02 (0.34), residues: 224 sheet: -1.22 (0.40), residues: 158 loop : -1.27 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 484 TYR 0.012 0.001 TYR B 313 PHE 0.029 0.001 PHE B 285 TRP 0.007 0.001 TRP B 687 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5928) covalent geometry : angle 0.58634 ( 8058) hydrogen bonds : bond 0.03472 ( 238) hydrogen bonds : angle 5.35746 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 34 time to evaluate : 0.139 Fit side-chains REVERT: B 161 CYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7062 (m) REVERT: B 265 MET cc_start: 0.8399 (mtm) cc_final: 0.8195 (mtp) REVERT: B 266 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8068 (tp) REVERT: B 284 MET cc_start: 0.7819 (mtt) cc_final: 0.7294 (tmm) REVERT: B 323 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8296 (tp) REVERT: B 397 MET cc_start: 0.3915 (ptp) cc_final: 0.3691 (ptp) REVERT: B 462 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8414 (mmpt) REVERT: B 622 MET cc_start: 0.7332 (mmm) cc_final: 0.6740 (mmm) outliers start: 28 outliers final: 11 residues processed: 57 average time/residue: 0.3075 time to fit residues: 18.6950 Evaluate side-chains 45 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 468 LYS Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN B 430 HIS B 758 GLN B 845 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.106646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.087219 restraints weight = 14295.725| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.80 r_work: 0.3480 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5928 Z= 0.136 Angle : 0.594 11.663 8058 Z= 0.292 Chirality : 0.044 0.161 909 Planarity : 0.004 0.041 1009 Dihedral : 8.675 88.912 854 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.49 % Allowed : 21.24 % Favored : 75.28 % 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: -0.70 (0.31), residues: 692 helix: 1.18 (0.34), residues: 223 sheet: -1.16 (0.40), residues: 157 loop : -1.26 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.011 0.001 TYR B 313 PHE 0.009 0.001 PHE B 648 TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5928) covalent geometry : angle 0.59371 ( 8058) hydrogen bonds : bond 0.03340 ( 238) hydrogen bonds : angle 5.20166 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.200 Fit side-chains REVERT: B 161 CYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7173 (m) REVERT: B 266 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8032 (tp) REVERT: B 320 VAL cc_start: 0.7954 (t) cc_final: 0.7556 (t) REVERT: B 323 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8345 (tp) REVERT: B 397 MET cc_start: 0.3545 (ptp) cc_final: 0.3339 (ptp) REVERT: B 462 LYS cc_start: 0.8646 (mmtp) cc_final: 0.8337 (mmpt) outliers start: 22 outliers final: 11 residues processed: 56 average time/residue: 0.2753 time to fit residues: 16.6109 Evaluate side-chains 46 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 468 LYS Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 37 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.0070 chunk 46 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN B 758 GLN B 845 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.107980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.089045 restraints weight = 14284.685| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.76 r_work: 0.3503 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5928 Z= 0.112 Angle : 0.604 11.437 8058 Z= 0.293 Chirality : 0.044 0.175 909 Planarity : 0.004 0.040 1009 Dihedral : 8.594 88.987 854 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.49 % Allowed : 22.03 % Favored : 74.48 % 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: -0.58 (0.32), residues: 692 helix: 1.35 (0.34), residues: 223 sheet: -1.14 (0.41), residues: 157 loop : -1.23 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.012 0.001 TYR B 313 PHE 0.028 0.001 PHE B 285 TRP 0.007 0.001 TRP B 687 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5928) covalent geometry : angle 0.60388 ( 8058) hydrogen bonds : bond 0.03135 ( 238) hydrogen bonds : angle 5.03599 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.140 Fit side-chains REVERT: B 161 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7167 (m) REVERT: B 266 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7996 (tt) REVERT: B 284 MET cc_start: 0.7772 (mtt) cc_final: 0.7256 (tmm) REVERT: B 323 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8448 (tp) REVERT: B 397 MET cc_start: 0.3733 (ptp) cc_final: 0.3393 (ptp) REVERT: B 462 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8411 (mmpt) REVERT: B 622 MET cc_start: 0.7015 (mmm) cc_final: 0.6511 (mmm) REVERT: B 845 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7916 (tp-100) REVERT: B 853 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8227 (mm) outliers start: 22 outliers final: 6 residues processed: 57 average time/residue: 0.2944 time to fit residues: 18.0248 Evaluate side-chains 46 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 853 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN B 758 GLN B 845 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.105952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.086392 restraints weight = 14070.917| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.80 r_work: 0.3476 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5928 Z= 0.134 Angle : 0.618 10.814 8058 Z= 0.302 Chirality : 0.045 0.171 909 Planarity : 0.004 0.040 1009 Dihedral : 8.613 87.806 854 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.69 % Allowed : 23.14 % Favored : 74.17 % 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: -0.58 (0.32), residues: 692 helix: 1.33 (0.34), residues: 223 sheet: -1.13 (0.41), residues: 157 loop : -1.21 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 756 TYR 0.011 0.001 TYR B 313 PHE 0.032 0.001 PHE B 285 TRP 0.008 0.001 TRP B 687 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5928) covalent geometry : angle 0.61776 ( 8058) hydrogen bonds : bond 0.03225 ( 238) hydrogen bonds : angle 5.07044 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 161 CYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7189 (m) REVERT: B 266 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7964 (tt) REVERT: B 284 MET cc_start: 0.7784 (mtt) cc_final: 0.7290 (tmm) REVERT: B 323 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8397 (tp) REVERT: B 397 MET cc_start: 0.3563 (ptp) cc_final: 0.3286 (ptp) REVERT: B 462 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8414 (mmpt) REVERT: B 551 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7443 (t) REVERT: B 622 MET cc_start: 0.7147 (mmm) cc_final: 0.6546 (mmm) outliers start: 17 outliers final: 6 residues processed: 53 average time/residue: 0.3403 time to fit residues: 19.2833 Evaluate side-chains 44 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.104851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.085873 restraints weight = 14443.532| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.78 r_work: 0.3440 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5928 Z= 0.169 Angle : 0.649 10.911 8058 Z= 0.319 Chirality : 0.046 0.182 909 Planarity : 0.004 0.041 1009 Dihedral : 8.650 86.142 854 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 24.09 % Favored : 73.85 % 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: -0.72 (0.32), residues: 692 helix: 1.22 (0.34), residues: 222 sheet: -1.14 (0.41), residues: 157 loop : -1.34 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 756 TYR 0.013 0.001 TYR B 693 PHE 0.036 0.002 PHE B 285 TRP 0.008 0.001 TRP B 687 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5928) covalent geometry : angle 0.64947 ( 8058) hydrogen bonds : bond 0.03385 ( 238) hydrogen bonds : angle 5.25453 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.189 Fit side-chains REVERT: B 161 CYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7013 (m) REVERT: B 266 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8061 (tt) REVERT: B 284 MET cc_start: 0.7788 (mtt) cc_final: 0.7246 (tmm) REVERT: B 323 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8497 (tp) REVERT: B 397 MET cc_start: 0.3979 (ptp) cc_final: 0.3610 (ptp) REVERT: B 462 LYS cc_start: 0.8648 (mmtp) cc_final: 0.8404 (mmpt) outliers start: 13 outliers final: 6 residues processed: 45 average time/residue: 0.3264 time to fit residues: 15.7300 Evaluate side-chains 41 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 46 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.106836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.088275 restraints weight = 14548.690| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.80 r_work: 0.3479 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5928 Z= 0.118 Angle : 0.648 13.003 8058 Z= 0.307 Chirality : 0.045 0.188 909 Planarity : 0.004 0.040 1009 Dihedral : 8.573 87.048 854 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.06 % Allowed : 24.41 % Favored : 73.53 % 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: -0.58 (0.32), residues: 692 helix: 1.36 (0.35), residues: 223 sheet: -1.12 (0.41), residues: 154 loop : -1.25 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 756 TYR 0.011 0.001 TYR B 313 PHE 0.031 0.001 PHE B 285 TRP 0.010 0.001 TRP B 687 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5928) covalent geometry : angle 0.64772 ( 8058) hydrogen bonds : bond 0.03107 ( 238) hydrogen bonds : angle 5.07230 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.231 Fit side-chains REVERT: B 161 CYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7000 (m) REVERT: B 284 MET cc_start: 0.7969 (mtt) cc_final: 0.7422 (tmm) REVERT: B 323 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8581 (tp) REVERT: B 397 MET cc_start: 0.3894 (ptp) cc_final: 0.3684 (ptp) REVERT: B 462 LYS cc_start: 0.8702 (mmtp) cc_final: 0.8422 (mmpt) REVERT: B 622 MET cc_start: 0.6948 (mmm) cc_final: 0.6426 (mmm) REVERT: B 853 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8324 (mm) outliers start: 13 outliers final: 5 residues processed: 43 average time/residue: 0.2952 time to fit residues: 13.7097 Evaluate side-chains 37 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 853 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 11 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.107697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.088938 restraints weight = 14351.545| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.83 r_work: 0.3487 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5928 Z= 0.116 Angle : 0.674 18.824 8058 Z= 0.310 Chirality : 0.045 0.201 909 Planarity : 0.004 0.039 1009 Dihedral : 8.540 87.024 854 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.58 % Allowed : 24.88 % Favored : 73.53 % 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: -0.57 (0.32), residues: 692 helix: 1.38 (0.34), residues: 223 sheet: -1.12 (0.40), residues: 154 loop : -1.25 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 756 TYR 0.012 0.001 TYR B 313 PHE 0.009 0.001 PHE B 648 TRP 0.011 0.001 TRP B 687 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5928) covalent geometry : angle 0.67413 ( 8058) hydrogen bonds : bond 0.03060 ( 238) hydrogen bonds : angle 5.05856 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.01 seconds wall clock time: 24 minutes 7.71 seconds (1447.71 seconds total)