Starting phenix.real_space_refine on Fri Sep 11 00:30:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z52_14513/09_2026/7z52_14513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z52_14513/09_2026/7z52_14513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z52_14513/09_2026/7z52_14513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z52_14513/09_2026/7z52_14513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z52_14513/09_2026/7z52_14513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z52_14513/09_2026/7z52_14513.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z52_14513/09_2026/7z52_14513.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z52_14513/09_2026/7z52_14513.cif" } resolution = 3.4 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= 0.003 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 45 5.16 5 C 3731 2.51 5 N 1002 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5911 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5494 Classifications: {'peptide': 706} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 680} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 8, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNAv2': 5} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "A" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 290 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 36} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 1.69, per 1000 atoms: 0.29 Number of scatterers: 5911 At special positions: 0 Unit cell: (87.6736, 88.5248, 77.4592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 7 15.00 O 1126 8.00 N 1002 7.00 C 3731 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: 0.55 Conformation dependent library (CDL) restraints added in 399.3 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 50.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 162 through 166 removed outlier: 4.065A pdb=" N GLY B 166 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 181 removed outlier: 4.528A pdb=" N ALA B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.748A pdb=" N GLU B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 238 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.807A pdb=" N GLU B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.676A pdb=" N PHE B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.637A pdb=" N PHE B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.504A pdb=" N ILE B 377 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 407 removed outlier: 3.546A pdb=" N CYS B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 430 removed outlier: 3.889A pdb=" N ASN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 removed outlier: 4.135A pdb=" N ASP B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 431 through 436' Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.690A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 460 through 474 removed outlier: 3.636A pdb=" N GLU B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 removed outlier: 3.535A pdb=" N ALA B 486 " --> pdb=" O GLU B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 580 through 587 removed outlier: 3.656A pdb=" N MET B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 Processing helix chain 'B' and resid 832 through 843 removed outlier: 3.998A pdb=" N ARG B 843 " --> pdb=" O LEU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 862 Processing helix chain 'B' and resid 871 through 878 removed outlier: 3.617A pdb=" N VAL B 876 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 895 Processing helix chain 'B' and resid 902 through 907 Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 925 through 948 Proline residue: B 931 - end of helix removed outlier: 3.528A pdb=" N VAL B 945 " --> pdb=" O ARG B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 962 removed outlier: 4.008A pdb=" N PHE B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 974 Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 989 through 1012 removed outlier: 3.540A pdb=" N GLN B1009 " --> pdb=" O ARG B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1029 removed outlier: 3.600A pdb=" N PHE B1023 " --> pdb=" O LEU B1019 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B1024 " --> pdb=" O GLU B1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 668 removed outlier: 3.641A pdb=" N PHE A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.674A pdb=" N LEU A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 99 through 101 removed outlier: 6.765A pdb=" N VAL B 157 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER B 283 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 159 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG B 184 " --> pdb=" O TRP B 248 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ILE B 250 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 186 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY B 210 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR B 228 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N MET B 212 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 332 removed outlier: 7.003A pdb=" N HIS B 318 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 496 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET B 538 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE B 498 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 390 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 389 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA B 481 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 391 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY B 453 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 502 through 504 245 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.76 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: 1865 1.34 - 1.45: 784 1.45 - 1.57: 3293 1.57 - 1.69: 13 1.69 - 1.81: 75 Bond restraints: 6030 Sorted by residual: bond pdb=" O3A ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" O5' ANP B2001 " pdb=" PA ANP B2001 " ideal model delta sigma weight residual 1.655 1.580 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.03e+00 bond pdb=" N GLN B 387 " pdb=" CA GLN B 387 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.44e-02 4.82e+03 7.41e+00 bond pdb=" O2B ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.87e+00 ... (remaining 6025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 8020 2.17 - 4.35: 131 4.35 - 6.52: 20 6.52 - 8.69: 5 8.69 - 10.87: 1 Bond angle restraints: 8177 Sorted by residual: angle pdb=" N VAL B 601 " pdb=" CA VAL B 601 " pdb=" C VAL B 601 " ideal model delta sigma weight residual 112.96 107.96 5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" C HIS B 300 " pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" O1B ANP B2001 " pdb=" PB ANP B2001 " pdb=" O2B ANP B2001 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N PRO B 97 " pdb=" CD PRO B 97 " pdb=" CG PRO B 97 " ideal model delta sigma weight residual 103.20 98.02 5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO B 97 " pdb=" N PRO B 97 " pdb=" CD PRO B 97 " ideal model delta sigma weight residual 112.00 107.53 4.47 1.40e+00 5.10e-01 1.02e+01 ... (remaining 8172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3279 18.00 - 35.99: 296 35.99 - 53.98: 50 53.98 - 71.98: 17 71.98 - 89.97: 8 Dihedral angle restraints: 3650 sinusoidal: 1470 harmonic: 2180 Sorted by residual: dihedral pdb=" C4' U R 1 " pdb=" C3' U R 1 " pdb=" C2' U R 1 " pdb=" C1' U R 1 " ideal model delta sinusoidal sigma weight residual 36.35 -37.77 74.12 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' U R 5 " pdb=" C3' U R 5 " pdb=" C2' U R 5 " pdb=" C1' U R 5 " ideal model delta sinusoidal sigma weight residual 36.34 -34.85 71.20 1 3.10e+00 1.04e-01 6.77e+02 dihedral pdb=" O4' U R 1 " pdb=" C4' U R 1 " pdb=" C3' U R 1 " pdb=" C2' U R 1 " ideal model delta sinusoidal sigma weight residual -35.15 26.16 -61.31 1 4.00e+00 6.25e-02 3.12e+02 ... (remaining 3647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 759 0.056 - 0.112: 153 0.112 - 0.168: 16 0.168 - 0.224: 0 0.224 - 0.281: 10 Chirality restraints: 938 Sorted by residual: chirality pdb=" C3' U R 1 " pdb=" C4' U R 1 " pdb=" O3' U R 1 " pdb=" C2' U R 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2' U R 1 " pdb=" C3' U R 1 " pdb=" O2' U R 1 " pdb=" C1' U R 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2' U R 5 " pdb=" C3' U R 5 " pdb=" O2' U R 5 " pdb=" C1' U R 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 935 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 921 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO B 922 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 922 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 922 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 560 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ASN B 560 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN B 560 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 561 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 598 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 599 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 599 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 599 " -0.022 5.00e-02 4.00e+02 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 615 2.75 - 3.29: 5722 3.29 - 3.82: 9193 3.82 - 4.36: 11169 4.36 - 4.90: 19323 Nonbonded interactions: 46022 Sorted by model distance: nonbonded pdb=" O LEU B 404 " pdb=" OG1 THR B 407 " model vdw 2.209 3.040 nonbonded pdb=" O THR B 972 " pdb=" OG1 THR B 975 " model vdw 2.269 3.040 nonbonded pdb=" NE2 GLN B 144 " pdb=" O GLY B 166 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASN B 572 " pdb=" NH2 ARG B 575 " model vdw 2.290 3.120 nonbonded pdb=" NZ LYS B 167 " pdb=" O SER B 283 " model vdw 2.291 3.120 ... (remaining 46017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 0.143 6030 Z= 0.205 Angle : 0.683 10.868 8177 Z= 0.352 Chirality : 0.049 0.281 938 Planarity : 0.004 0.049 1033 Dihedral : 15.001 89.974 2232 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.76 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.69 (0.30), residues: 738 helix: -0.40 (0.28), residues: 362 sheet: 0.44 (0.60), residues: 82 loop : -2.51 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 502 TYR 0.011 0.001 TYR B 590 PHE 0.015 0.002 PHE B 563 TRP 0.015 0.001 TRP B 266 HIS 0.003 0.001 HIS B 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 6030) covalent geometry : angle 0.68270 / 0.35 ( 8177) hydrogen bonds : bond 0.17008 / 12.29 ( 245) hydrogen bonds : angle 5.36687 / 3.88 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 TYR cc_start: 0.8664 (t80) cc_final: 0.8450 (t80) REVERT: B 244 ARG cc_start: 0.6399 (ttm-80) cc_final: 0.6030 (tpp-160) REVERT: B 256 TYR cc_start: 0.6257 (m-80) cc_final: 0.6005 (m-80) REVERT: B 569 MET cc_start: 0.8216 (ttm) cc_final: 0.7884 (ttm) REVERT: B 590 TYR cc_start: 0.8272 (t80) cc_final: 0.7560 (t80) REVERT: B 935 MET cc_start: 0.8169 (tmm) cc_final: 0.7894 (tmm) REVERT: B 987 ASP cc_start: 0.7079 (p0) cc_final: 0.6339 (p0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0859 time to fit residues: 13.6061 Evaluate side-chains 71 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 ASN B 207 GLN B 255 HIS B 291 GLN ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107388 restraints weight = 7487.224| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.13 r_work: 0.3079 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6030 Z= 0.186 Angle : 0.649 10.406 8177 Z= 0.324 Chirality : 0.048 0.439 938 Planarity : 0.004 0.037 1033 Dihedral : 8.609 154.302 859 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.67 % Favored : 91.19 % Rotamer: Outliers : 1.80 % Allowed : 7.36 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.40 (0.30), residues: 738 helix: -0.11 (0.28), residues: 370 sheet: 0.35 (0.61), residues: 83 loop : -2.42 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 860 TYR 0.012 0.001 TYR B 319 PHE 0.013 0.002 PHE B 394 TRP 0.005 0.001 TRP B 266 HIS 0.003 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 6030) covalent geometry : angle 0.64894 / 0.32 ( 8177) hydrogen bonds : bond 0.04598 / 3.14 ( 245) hydrogen bonds : angle 4.24467 / 3.00 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 120 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7237 (tm-30) REVERT: B 203 TYR cc_start: 0.8882 (t80) cc_final: 0.8660 (t80) REVERT: B 440 GLN cc_start: 0.7230 (mp10) cc_final: 0.6767 (tp40) REVERT: B 569 MET cc_start: 0.8661 (ttm) cc_final: 0.8424 (ttm) REVERT: B 590 TYR cc_start: 0.8767 (t80) cc_final: 0.7711 (t80) REVERT: B 872 MET cc_start: 0.8287 (tpp) cc_final: 0.7951 (tpp) REVERT: B 1042 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8233 (mp) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.0727 time to fit residues: 7.5414 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain A residue 663 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 58 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 GLN ** B 965 HIS ** 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 = 0.3494 r_free = 0.3494 target = 0.126856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101739 restraints weight = 7611.183| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.98 r_work: 0.3007 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 6030 Z= 0.260 Angle : 0.711 11.843 8177 Z= 0.360 Chirality : 0.051 0.363 938 Planarity : 0.004 0.036 1033 Dihedral : 9.100 159.364 859 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.33 % Rotamer: Outliers : 2.62 % Allowed : 11.46 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.43 (0.30), residues: 738 helix: -0.14 (0.27), residues: 368 sheet: 0.06 (0.61), residues: 83 loop : -2.31 (0.32), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 687 TYR 0.017 0.002 TYR B 319 PHE 0.024 0.002 PHE B 563 TRP 0.006 0.002 TRP B 248 HIS 0.007 0.002 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.26 ( 6030) covalent geometry : angle 0.71137 / 0.36 ( 8177) hydrogen bonds : bond 0.05483 / 3.78 ( 245) hydrogen bonds : angle 4.32692 / 3.06 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.230 Fit side-chains REVERT: B 120 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7359 (tm-30) REVERT: B 440 GLN cc_start: 0.7364 (mp10) cc_final: 0.6993 (tp40) REVERT: B 550 GLN cc_start: 0.7820 (mt0) cc_final: 0.7614 (pt0) REVERT: B 590 TYR cc_start: 0.8857 (t80) cc_final: 0.7820 (t80) REVERT: B 867 SER cc_start: 0.8246 (m) cc_final: 0.7700 (t) REVERT: B 872 MET cc_start: 0.8357 (tpp) cc_final: 0.8041 (tpp) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.0661 time to fit residues: 7.2873 Evaluate side-chains 72 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 885 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 965 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 = 0.3498 r_free = 0.3498 target = 0.127494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101835 restraints weight = 7703.939| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.05 r_work: 0.3029 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6030 Z= 0.186 Angle : 0.618 9.740 8177 Z= 0.311 Chirality : 0.047 0.275 938 Planarity : 0.004 0.032 1033 Dihedral : 8.693 152.592 859 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 2.95 % Allowed : 12.93 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.16 (0.31), residues: 738 helix: 0.16 (0.27), residues: 369 sheet: 0.06 (0.61), residues: 83 loop : -2.27 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.017 0.001 TYR B 203 PHE 0.015 0.002 PHE B 563 TRP 0.005 0.001 TRP B 266 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 6030) covalent geometry : angle 0.61756 / 0.31 ( 8177) hydrogen bonds : bond 0.04428 / 3.07 ( 245) hydrogen bonds : angle 4.02292 / 2.83 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.241 Fit side-chains REVERT: B 120 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7251 (tm-30) REVERT: B 201 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: B 440 GLN cc_start: 0.7330 (mp10) cc_final: 0.6940 (tp40) REVERT: B 550 GLN cc_start: 0.7735 (mt0) cc_final: 0.7513 (pt0) REVERT: B 590 TYR cc_start: 0.8875 (t80) cc_final: 0.7844 (t80) REVERT: B 867 SER cc_start: 0.8196 (m) cc_final: 0.7661 (t) REVERT: B 872 MET cc_start: 0.8282 (tpp) cc_final: 0.8025 (tpp) outliers start: 18 outliers final: 10 residues processed: 80 average time/residue: 0.0709 time to fit residues: 7.9268 Evaluate side-chains 73 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 965 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 = 0.3528 r_free = 0.3528 target = 0.129771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103688 restraints weight = 7768.779| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.07 r_work: 0.3045 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6030 Z= 0.149 Angle : 0.585 9.443 8177 Z= 0.293 Chirality : 0.045 0.257 938 Planarity : 0.003 0.033 1033 Dihedral : 8.460 150.504 859 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.13 % Favored : 91.73 % Rotamer: Outliers : 3.93 % Allowed : 12.77 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.94 (0.31), residues: 738 helix: 0.38 (0.28), residues: 370 sheet: 0.13 (0.61), residues: 83 loop : -2.22 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 510 TYR 0.010 0.001 TYR B 319 PHE 0.011 0.001 PHE B 563 TRP 0.006 0.001 TRP B 511 HIS 0.004 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 6030) covalent geometry : angle 0.58512 / 0.29 ( 8177) hydrogen bonds : bond 0.03928 / 2.72 ( 245) hydrogen bonds : angle 3.81045 / 2.68 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.226 Fit side-chains REVERT: B 120 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7259 (tm-30) REVERT: B 440 GLN cc_start: 0.7324 (mp10) cc_final: 0.6938 (tp40) REVERT: B 550 GLN cc_start: 0.7687 (mt0) cc_final: 0.7486 (pt0) REVERT: B 590 TYR cc_start: 0.8865 (t80) cc_final: 0.7808 (t80) REVERT: B 867 SER cc_start: 0.8193 (m) cc_final: 0.7654 (t) REVERT: B 1031 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8664 (mtpp) outliers start: 24 outliers final: 13 residues processed: 82 average time/residue: 0.0596 time to fit residues: 7.1586 Evaluate side-chains 76 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1031 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.0270 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 965 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 = 0.3555 r_free = 0.3555 target = 0.131894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106146 restraints weight = 7622.661| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.04 r_work: 0.3084 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6030 Z= 0.117 Angle : 0.545 9.031 8177 Z= 0.274 Chirality : 0.044 0.250 938 Planarity : 0.003 0.034 1033 Dihedral : 8.178 146.830 859 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.28 % Rotamer: Outliers : 3.27 % Allowed : 14.24 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.71 (0.31), residues: 738 helix: 0.56 (0.28), residues: 370 sheet: 0.39 (0.62), residues: 82 loop : -2.15 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 351 TYR 0.007 0.001 TYR B 199 PHE 0.011 0.001 PHE B 504 TRP 0.007 0.001 TRP B 295 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6030) covalent geometry : angle 0.54535 / 0.27 ( 8177) hydrogen bonds : bond 0.03420 / 2.36 ( 245) hydrogen bonds : angle 3.63305 / 2.55 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.177 Fit side-chains REVERT: B 120 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7215 (tm-30) REVERT: B 385 ASN cc_start: 0.8468 (m-40) cc_final: 0.7969 (t0) REVERT: B 440 GLN cc_start: 0.7267 (mp10) cc_final: 0.6914 (tp40) REVERT: B 590 TYR cc_start: 0.8867 (t80) cc_final: 0.7795 (t80) REVERT: B 867 SER cc_start: 0.8162 (m) cc_final: 0.7614 (t) outliers start: 20 outliers final: 12 residues processed: 78 average time/residue: 0.0618 time to fit residues: 6.9243 Evaluate side-chains 75 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 GLN ** B 965 HIS ** 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 = 0.3525 r_free = 0.3525 target = 0.129448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103562 restraints weight = 7748.086| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.07 r_work: 0.3034 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6030 Z= 0.157 Angle : 0.580 9.810 8177 Z= 0.290 Chirality : 0.045 0.253 938 Planarity : 0.003 0.033 1033 Dihedral : 8.311 148.269 859 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.40 % Favored : 91.46 % Rotamer: Outliers : 3.44 % Allowed : 15.06 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.74 (0.31), residues: 738 helix: 0.54 (0.28), residues: 371 sheet: 0.27 (0.62), residues: 83 loop : -2.15 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 510 TYR 0.020 0.001 TYR B 203 PHE 0.012 0.001 PHE B 563 TRP 0.005 0.001 TRP B 266 HIS 0.004 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 6030) covalent geometry : angle 0.58034 / 0.29 ( 8177) hydrogen bonds : bond 0.03990 / 2.76 ( 245) hydrogen bonds : angle 3.71491 / 2.60 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.195 Fit side-chains REVERT: B 266 TRP cc_start: 0.7844 (OUTLIER) cc_final: 0.6829 (t-100) REVERT: B 440 GLN cc_start: 0.7304 (mp10) cc_final: 0.6938 (tp40) REVERT: B 590 TYR cc_start: 0.8875 (t80) cc_final: 0.7802 (t80) REVERT: B 867 SER cc_start: 0.8202 (m) cc_final: 0.7658 (t) outliers start: 21 outliers final: 16 residues processed: 80 average time/residue: 0.0530 time to fit residues: 6.2592 Evaluate side-chains 80 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 266 TRP Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 965 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 = 0.3547 r_free = 0.3547 target = 0.131357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105625 restraints weight = 7596.484| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.06 r_work: 0.3074 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6030 Z= 0.127 Angle : 0.554 10.274 8177 Z= 0.276 Chirality : 0.044 0.245 938 Planarity : 0.003 0.034 1033 Dihedral : 8.146 146.328 859 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 3.44 % Allowed : 15.22 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.66 (0.32), residues: 738 helix: 0.74 (0.28), residues: 365 sheet: 0.30 (0.62), residues: 82 loop : -2.25 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.008 0.001 TYR B 199 PHE 0.009 0.001 PHE B 143 TRP 0.005 0.001 TRP B 295 HIS 0.003 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 6030) covalent geometry : angle 0.55371 / 0.28 ( 8177) hydrogen bonds : bond 0.03530 / 2.45 ( 245) hydrogen bonds : angle 3.58772 / 2.51 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.309 Fit side-chains REVERT: B 266 TRP cc_start: 0.7764 (OUTLIER) cc_final: 0.6680 (t-100) REVERT: B 385 ASN cc_start: 0.8467 (m-40) cc_final: 0.7993 (t0) REVERT: B 440 GLN cc_start: 0.7280 (mp10) cc_final: 0.6926 (tp40) REVERT: B 590 TYR cc_start: 0.8861 (t80) cc_final: 0.7801 (t80) REVERT: B 867 SER cc_start: 0.8176 (m) cc_final: 0.7627 (t) outliers start: 21 outliers final: 15 residues processed: 78 average time/residue: 0.0565 time to fit residues: 6.5877 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 266 TRP Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 965 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 = 0.3520 r_free = 0.3520 target = 0.129162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103420 restraints weight = 7744.590| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.07 r_work: 0.3035 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6030 Z= 0.168 Angle : 0.595 10.755 8177 Z= 0.298 Chirality : 0.045 0.262 938 Planarity : 0.003 0.033 1033 Dihedral : 8.319 147.932 859 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 3.27 % Allowed : 15.88 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.77 (0.31), residues: 738 helix: 0.53 (0.28), residues: 371 sheet: 0.10 (0.62), residues: 83 loop : -2.13 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.011 0.001 TYR B 319 PHE 0.013 0.001 PHE B 563 TRP 0.005 0.001 TRP B 266 HIS 0.005 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 6030) covalent geometry : angle 0.59527 / 0.30 ( 8177) hydrogen bonds : bond 0.04117 / 2.85 ( 245) hydrogen bonds : angle 3.74449 / 2.62 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.234 Fit side-chains REVERT: B 266 TRP cc_start: 0.7851 (OUTLIER) cc_final: 0.7062 (t-100) REVERT: B 440 GLN cc_start: 0.7341 (mp10) cc_final: 0.6978 (tp40) REVERT: B 590 TYR cc_start: 0.8882 (t80) cc_final: 0.7834 (t80) REVERT: B 867 SER cc_start: 0.8247 (m) cc_final: 0.7699 (t) outliers start: 20 outliers final: 17 residues processed: 76 average time/residue: 0.0577 time to fit residues: 6.4691 Evaluate side-chains 79 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 266 TRP Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 965 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 = 0.3555 r_free = 0.3555 target = 0.132066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106412 restraints weight = 7652.450| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.07 r_work: 0.3079 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6030 Z= 0.115 Angle : 0.548 10.503 8177 Z= 0.273 Chirality : 0.043 0.241 938 Planarity : 0.003 0.034 1033 Dihedral : 8.047 144.955 859 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 2.78 % Allowed : 16.53 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.59 (0.32), residues: 738 helix: 0.82 (0.29), residues: 365 sheet: 0.29 (0.62), residues: 82 loop : -2.23 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 244 TYR 0.007 0.001 TYR B 199 PHE 0.009 0.001 PHE B 143 TRP 0.006 0.001 TRP B 295 HIS 0.003 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.11 ( 6030) covalent geometry : angle 0.54788 / 0.27 ( 8177) hydrogen bonds : bond 0.03322 / 2.29 ( 245) hydrogen bonds : angle 3.56045 / 2.49 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.227 Fit side-chains REVERT: B 266 TRP cc_start: 0.7743 (OUTLIER) cc_final: 0.6608 (t-100) REVERT: B 385 ASN cc_start: 0.8440 (m-40) cc_final: 0.7970 (t0) REVERT: B 440 GLN cc_start: 0.7288 (mp10) cc_final: 0.6942 (tp40) REVERT: B 590 TYR cc_start: 0.8844 (t80) cc_final: 0.7749 (t80) REVERT: B 867 SER cc_start: 0.8147 (m) cc_final: 0.7590 (t) REVERT: B 956 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6818 (mm-30) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.0587 time to fit residues: 6.7497 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 266 TRP Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 1014 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 0.0050 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 GLN ** B 965 HIS ** 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 = 0.3581 r_free = 0.3581 target = 0.134245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108934 restraints weight = 7574.480| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.01 r_work: 0.3104 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6030 Z= 0.103 Angle : 0.540 11.723 8177 Z= 0.268 Chirality : 0.042 0.235 938 Planarity : 0.003 0.035 1033 Dihedral : 7.820 142.227 859 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 2.62 % Allowed : 16.37 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.47 (0.32), residues: 738 helix: 0.94 (0.29), residues: 365 sheet: 0.37 (0.62), residues: 82 loop : -2.22 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 244 TYR 0.019 0.001 TYR B 203 PHE 0.015 0.001 PHE B1036 TRP 0.007 0.001 TRP B 295 HIS 0.002 0.001 HIS B 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 ( 6030) covalent geometry : angle 0.54036 / 0.27 ( 8177) hydrogen bonds : bond 0.03096 / 2.11 ( 245) hydrogen bonds : angle 3.48705 / 2.42 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.43 seconds wall clock time: 26 minutes 16.22 seconds (1576.22 seconds total)