Starting phenix.real_space_refine on Wed Sep 17 15:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge6_51291/09_2025/9ge6_51291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge6_51291/09_2025/9ge6_51291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ge6_51291/09_2025/9ge6_51291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge6_51291/09_2025/9ge6_51291.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ge6_51291/09_2025/9ge6_51291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge6_51291/09_2025/9ge6_51291.map" } resolution = 4.05 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= 0.001 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6162 2.51 5 N 1700 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6254 Classifications: {'peptide': 799} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 755} Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1696 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "C" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1696 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Time building chain proxies: 2.66, per 1000 atoms: 0.28 Number of scatterers: 9646 At special positions: 0 Unit cell: (126.085, 111.055, 108.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1742 8.00 N 1700 7.00 C 6162 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: 1.03 Conformation dependent library (CDL) restraints added in 347.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 56.3% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 12 through 50 Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.956A pdb=" N LEU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.821A pdb=" N GLY A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 231 through 280 removed outlier: 3.800A pdb=" N ARG A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 321 Processing helix chain 'A' and resid 334 through 361 removed outlier: 5.711A pdb=" N ARG A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 378 through 399 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 401 through 432 Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 449 through 483 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.533A pdb=" N LEU A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 583 Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 662 through 702 Processing helix chain 'A' and resid 703 through 718 Processing helix chain 'A' and resid 720 through 757 Processing helix chain 'A' and resid 766 through 793 removed outlier: 3.541A pdb=" N TRP A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Proline residue: A 774 - end of helix Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.933A pdb=" N LEU A 798 " --> pdb=" O GLY A 795 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 799 " --> pdb=" O LYS A 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 795 through 799' Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.576A pdb=" N HIS B 21 " --> pdb=" O GLN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 104 through 117 Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 119 through 134 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 148 through 163 removed outlier: 4.660A pdb=" N GLY B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.776A pdb=" N GLU B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.547A pdb=" N CYS B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 104 through 116 Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 119 through 134 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.942A pdb=" N LEU C 140 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 Processing helix chain 'C' and resid 148 through 163 removed outlier: 4.771A pdb=" N GLY C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 4.362A pdb=" N ASN C 176 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 197 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.146A pdb=" N ALA C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 55 through 59 current: chain 'A' and resid 94 through 102 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 94 through 102 current: chain 'A' and resid 149 through 159 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 495 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 492 through 495 current: chain 'A' and resid 533 through 534 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 533 through 534 current: chain 'A' and resid 599 through 608 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 16 removed outlier: 6.452A pdb=" N LEU B 12 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B 27 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS B 14 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.386A pdb=" N GLY B 91 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASP B 171 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 93 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR B 38 " --> pdb=" O ARG B 215 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 217 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA B 40 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU B 219 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 42 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 23 through 33 removed outlier: 5.957A pdb=" N LYS C 14 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR C 27 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU C 12 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 29 " --> pdb=" O HIS C 10 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS C 10 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 31 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 8 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL C 9 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N SER C 68 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS C 11 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU C 66 " --> pdb=" O HIS C 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 93 removed outlier: 6.426A pdb=" N GLY C 91 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP C 171 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 93 " --> pdb=" O ASP C 171 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1554 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: 1.72 Time building geometry restraints manager: 1.27 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: 3217 1.34 - 1.46: 1484 1.46 - 1.58: 5051 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9826 Sorted by residual: bond pdb=" CB MET A 51 " pdb=" CG MET A 51 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CA LEU A 280 " pdb=" C LEU A 280 " ideal model delta sigma weight residual 1.523 1.500 0.024 1.80e-02 3.09e+03 1.74e+00 bond pdb=" CB GLN A 456 " pdb=" CG GLN A 456 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CG GLN A 456 " pdb=" CD GLN A 456 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.06e+00 ... (remaining 9821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12982 1.75 - 3.50: 275 3.50 - 5.26: 61 5.26 - 7.01: 13 7.01 - 8.76: 3 Bond angle restraints: 13334 Sorted by residual: angle pdb=" C VAL B 220 " pdb=" N ASN B 221 " pdb=" CA ASN B 221 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" CA MET A 176 " pdb=" CB MET A 176 " pdb=" CG MET A 176 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.63e+00 angle pdb=" C SER B 96 " pdb=" N PHE B 97 " pdb=" CA PHE B 97 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.60e+00 angle pdb=" C LYS C 88 " pdb=" N HIS C 89 " pdb=" CA HIS C 89 " ideal model delta sigma weight residual 122.15 114.52 7.63 2.83e+00 1.25e-01 7.27e+00 angle pdb=" C MET A 176 " pdb=" CA MET A 176 " pdb=" CB MET A 176 " ideal model delta sigma weight residual 110.43 114.89 -4.46 1.68e+00 3.54e-01 7.06e+00 ... (remaining 13329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 5289 16.29 - 32.59: 520 32.59 - 48.88: 82 48.88 - 65.18: 13 65.18 - 81.47: 12 Dihedral angle restraints: 5916 sinusoidal: 2376 harmonic: 3540 Sorted by residual: dihedral pdb=" CA GLU A 49 " pdb=" C GLU A 49 " pdb=" N PHE A 50 " pdb=" CA PHE A 50 " ideal model delta harmonic sigma weight residual 180.00 144.40 35.60 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CA PHE B 97 " pdb=" C PHE B 97 " pdb=" N MET B 98 " pdb=" CA MET B 98 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA SER B 96 " pdb=" C SER B 96 " pdb=" N PHE B 97 " pdb=" CA PHE B 97 " ideal model delta harmonic sigma weight residual 180.00 163.24 16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1085 0.037 - 0.073: 313 0.073 - 0.110: 129 0.110 - 0.147: 18 0.147 - 0.183: 4 Chirality restraints: 1549 Sorted by residual: chirality pdb=" CA PHE B 97 " pdb=" N PHE B 97 " pdb=" C PHE B 97 " pdb=" CB PHE B 97 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA GLU A 49 " pdb=" N GLU A 49 " pdb=" C GLU A 49 " pdb=" CB GLU A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA LEU C 111 " pdb=" N LEU C 111 " pdb=" C LEU C 111 " pdb=" CB LEU C 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1546 not shown) Planarity restraints: 1711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 473 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LEU A 473 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU A 473 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 474 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 50 " 0.014 2.00e-02 2.50e+03 1.83e-02 5.89e+00 pdb=" CG PHE A 50 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 50 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 50 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 50 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 456 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" CD GLN A 456 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLN A 456 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN A 456 " 0.011 2.00e-02 2.50e+03 ... (remaining 1708 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 167 2.64 - 3.21: 9682 3.21 - 3.77: 16598 3.77 - 4.34: 20791 4.34 - 4.90: 33527 Nonbonded interactions: 80765 Sorted by model distance: nonbonded pdb=" O VAL C 109 " pdb=" ND2 ASN C 162 " model vdw 2.080 3.120 nonbonded pdb=" O VAL A 522 " pdb=" OG SER A 634 " model vdw 2.194 3.040 nonbonded pdb=" O GLY C 48 " pdb=" OG1 THR C 51 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP A 145 " pdb=" OG1 THR A 150 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR B 27 " pdb=" OE1 GLN B 223 " model vdw 2.220 3.040 ... (remaining 80760 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.140 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9826 Z= 0.172 Angle : 0.653 8.762 13334 Z= 0.327 Chirality : 0.042 0.183 1549 Planarity : 0.004 0.033 1711 Dihedral : 13.386 81.470 3632 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.99 (0.24), residues: 1241 helix: 1.81 (0.21), residues: 616 sheet: -0.31 (0.41), residues: 156 loop : -0.51 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 653 TYR 0.007 0.001 TYR A 356 PHE 0.042 0.002 PHE A 50 TRP 0.015 0.001 TRP A 405 HIS 0.004 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9826) covalent geometry : angle 0.65322 (13334) hydrogen bonds : bond 0.13424 ( 537) hydrogen bonds : angle 5.21290 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7791 (m-80) cc_final: 0.6725 (t80) REVERT: A 51 MET cc_start: 0.3954 (tpt) cc_final: 0.3577 (tpt) REVERT: A 175 MET cc_start: 0.7973 (ttt) cc_final: 0.7361 (ttm) REVERT: A 297 MET cc_start: 0.8529 (mmt) cc_final: 0.8206 (mmp) REVERT: A 344 MET cc_start: 0.8576 (ppp) cc_final: 0.8282 (ppp) REVERT: A 704 MET cc_start: 0.8697 (mmp) cc_final: 0.8336 (mmm) REVERT: A 709 GLN cc_start: 0.8613 (pp30) cc_final: 0.8404 (pp30) REVERT: B 41 LEU cc_start: 0.8778 (tp) cc_final: 0.8557 (tt) REVERT: C 88 LYS cc_start: 0.9456 (tppp) cc_final: 0.9073 (tppp) REVERT: C 103 LEU cc_start: 0.9084 (mm) cc_final: 0.8880 (mt) REVERT: C 202 MET cc_start: 0.8503 (tpt) cc_final: 0.8195 (tpp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0940 time to fit residues: 21.0032 Evaluate side-chains 119 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0270 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 overall best weight: 2.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 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 = 0.3602 r_free = 0.3602 target = 0.065208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.045315 restraints weight = 56590.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046836 restraints weight = 35065.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.047851 restraints weight = 25140.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048584 restraints weight = 19960.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049004 restraints weight = 16926.382| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9826 Z= 0.157 Angle : 0.611 8.346 13334 Z= 0.309 Chirality : 0.041 0.167 1549 Planarity : 0.004 0.033 1711 Dihedral : 4.139 33.021 1333 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.97 (0.24), residues: 1241 helix: 1.73 (0.21), residues: 627 sheet: -0.40 (0.41), residues: 156 loop : -0.43 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.012 0.001 TYR A 356 PHE 0.037 0.002 PHE A 50 TRP 0.012 0.001 TRP A 339 HIS 0.005 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9826) covalent geometry : angle 0.61120 (13334) hydrogen bonds : bond 0.04815 ( 537) hydrogen bonds : angle 4.70513 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4629 (tpt) cc_final: 0.4357 (tpt) REVERT: A 175 MET cc_start: 0.7863 (ttt) cc_final: 0.7422 (ttm) REVERT: A 297 MET cc_start: 0.8523 (mmt) cc_final: 0.8186 (mmp) REVERT: A 344 MET cc_start: 0.8743 (ppp) cc_final: 0.8445 (tmm) REVERT: A 424 MET cc_start: 0.8742 (mmt) cc_final: 0.8535 (mmt) REVERT: A 465 MET cc_start: 0.8769 (mmp) cc_final: 0.8551 (mmm) REVERT: A 704 MET cc_start: 0.8716 (mmp) cc_final: 0.8366 (tpp) REVERT: A 709 GLN cc_start: 0.8754 (pp30) cc_final: 0.8500 (pp30) REVERT: B 124 ARG cc_start: 0.9106 (ptp-110) cc_final: 0.8871 (ptp-110) REVERT: C 88 LYS cc_start: 0.9424 (tppp) cc_final: 0.9065 (tppp) REVERT: C 104 ASN cc_start: 0.8918 (p0) cc_final: 0.8569 (p0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0968 time to fit residues: 21.0795 Evaluate side-chains 114 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 58 optimal weight: 50.0000 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 114 optimal weight: 0.2980 chunk 120 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 HIS B 108 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.065833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.046098 restraints weight = 55345.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.047755 restraints weight = 32688.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.048870 restraints weight = 22683.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.049629 restraints weight = 17548.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050079 restraints weight = 14673.458| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9826 Z= 0.130 Angle : 0.601 8.381 13334 Z= 0.300 Chirality : 0.041 0.191 1549 Planarity : 0.004 0.030 1711 Dihedral : 4.124 31.307 1333 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 1.01 (0.24), residues: 1241 helix: 1.76 (0.21), residues: 629 sheet: -0.26 (0.42), residues: 152 loop : -0.47 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 164 TYR 0.012 0.001 TYR A 356 PHE 0.070 0.002 PHE A 50 TRP 0.012 0.001 TRP A 339 HIS 0.010 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9826) covalent geometry : angle 0.60110 (13334) hydrogen bonds : bond 0.04499 ( 537) hydrogen bonds : angle 4.51633 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7979 (m-80) cc_final: 0.6713 (t80) REVERT: A 51 MET cc_start: 0.5016 (tpt) cc_final: 0.4474 (tpt) REVERT: A 297 MET cc_start: 0.8560 (mmt) cc_final: 0.8189 (mmp) REVERT: A 344 MET cc_start: 0.8855 (ppp) cc_final: 0.8538 (tmm) REVERT: A 424 MET cc_start: 0.8735 (mmt) cc_final: 0.8519 (mmt) REVERT: A 465 MET cc_start: 0.8872 (mmp) cc_final: 0.8638 (mmm) REVERT: A 704 MET cc_start: 0.8810 (mmp) cc_final: 0.8432 (tpp) REVERT: A 709 GLN cc_start: 0.9092 (pp30) cc_final: 0.8454 (pp30) REVERT: A 710 GLU cc_start: 0.8817 (tp30) cc_final: 0.8455 (tp30) REVERT: B 124 ARG cc_start: 0.9152 (ptp-110) cc_final: 0.8912 (ptp-110) REVERT: C 88 LYS cc_start: 0.9417 (tppp) cc_final: 0.9065 (tppp) REVERT: C 202 MET cc_start: 0.8570 (tpt) cc_final: 0.8339 (tpp) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.0950 time to fit residues: 21.0057 Evaluate side-chains 120 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 50.0000 chunk 48 optimal weight: 0.8980 chunk 106 optimal weight: 0.0000 chunk 45 optimal weight: 0.6980 overall best weight: 0.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 456 GLN ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 HIS B 146 GLN ** C 153 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.067582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.048364 restraints weight = 57775.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.049898 restraints weight = 36307.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.050949 restraints weight = 26191.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.051652 restraints weight = 20767.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052079 restraints weight = 17661.819| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9826 Z= 0.115 Angle : 0.588 9.602 13334 Z= 0.288 Chirality : 0.040 0.170 1549 Planarity : 0.003 0.028 1711 Dihedral : 4.024 28.242 1333 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 aren not related in a simple way. whole: 1.04 (0.24), residues: 1241 helix: 1.75 (0.21), residues: 629 sheet: 0.01 (0.40), residues: 170 loop : -0.52 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 653 TYR 0.011 0.001 TYR A 356 PHE 0.048 0.002 PHE A 50 TRP 0.011 0.001 TRP A 339 HIS 0.009 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9826) covalent geometry : angle 0.58810 (13334) hydrogen bonds : bond 0.04331 ( 537) hydrogen bonds : angle 4.39911 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7815 (m-80) cc_final: 0.6501 (t80) REVERT: A 51 MET cc_start: 0.4797 (tpt) cc_final: 0.4333 (tpt) REVERT: A 175 MET cc_start: 0.7857 (ttt) cc_final: 0.7494 (ttt) REVERT: A 297 MET cc_start: 0.8295 (mmt) cc_final: 0.7973 (mmp) REVERT: A 465 MET cc_start: 0.8845 (mmp) cc_final: 0.8635 (mmm) REVERT: A 709 GLN cc_start: 0.8973 (pp30) cc_final: 0.8289 (pp30) REVERT: A 710 GLU cc_start: 0.8484 (tp30) cc_final: 0.8187 (tp30) REVERT: B 124 ARG cc_start: 0.9077 (ptp-110) cc_final: 0.8768 (ptp-110) REVERT: B 125 ASN cc_start: 0.9056 (m110) cc_final: 0.8800 (m110) REVERT: B 128 LYS cc_start: 0.9259 (ptpp) cc_final: 0.9038 (pttm) REVERT: C 88 LYS cc_start: 0.9317 (tppp) cc_final: 0.9017 (tppp) REVERT: C 183 ASP cc_start: 0.8939 (p0) cc_final: 0.7746 (p0) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0920 time to fit residues: 21.5734 Evaluate side-chains 128 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 0.7980 chunk 14 optimal weight: 40.0000 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 652 ASN B 21 HIS B 108 ASN B 146 GLN C 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.064580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.045290 restraints weight = 58696.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.046747 restraints weight = 36887.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047738 restraints weight = 26757.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048389 restraints weight = 21360.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.048845 restraints weight = 18292.534| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9826 Z= 0.212 Angle : 0.664 8.816 13334 Z= 0.331 Chirality : 0.042 0.181 1549 Planarity : 0.004 0.034 1711 Dihedral : 4.156 26.788 1333 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 aren not related in a simple way. whole: 0.98 (0.24), residues: 1241 helix: 1.73 (0.21), residues: 628 sheet: -0.15 (0.39), residues: 181 loop : -0.53 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 179 TYR 0.008 0.001 TYR A 356 PHE 0.047 0.002 PHE A 50 TRP 0.016 0.002 TRP A 635 HIS 0.006 0.002 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9826) covalent geometry : angle 0.66401 (13334) hydrogen bonds : bond 0.04605 ( 537) hydrogen bonds : angle 4.57823 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7891 (m-80) cc_final: 0.6637 (t80) REVERT: A 51 MET cc_start: 0.4781 (tpt) cc_final: 0.4373 (tpt) REVERT: A 108 MET cc_start: 0.7530 (ptt) cc_final: 0.7064 (ptt) REVERT: A 175 MET cc_start: 0.8177 (ttt) cc_final: 0.7539 (ttm) REVERT: A 297 MET cc_start: 0.8407 (mmt) cc_final: 0.8104 (mmp) REVERT: A 301 LEU cc_start: 0.9482 (tp) cc_final: 0.9274 (tp) REVERT: A 682 GLU cc_start: 0.8633 (pp20) cc_final: 0.8363 (pp20) REVERT: B 124 ARG cc_start: 0.9082 (ptp-110) cc_final: 0.8839 (ptp-110) REVERT: C 39 ILE cc_start: 0.9155 (mm) cc_final: 0.8719 (tp) REVERT: C 61 ASP cc_start: 0.8886 (t0) cc_final: 0.8685 (t0) REVERT: C 88 LYS cc_start: 0.9426 (tppp) cc_final: 0.9048 (tppp) REVERT: C 179 ARG cc_start: 0.8633 (tpt90) cc_final: 0.8230 (tpm170) REVERT: C 183 ASP cc_start: 0.8964 (p0) cc_final: 0.7755 (p0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0942 time to fit residues: 20.1457 Evaluate side-chains 116 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 21 HIS B 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.065869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.046606 restraints weight = 58601.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.048124 restraints weight = 36535.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.049173 restraints weight = 26326.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.049868 restraints weight = 20850.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.050330 restraints weight = 17780.955| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9826 Z= 0.140 Angle : 0.608 7.837 13334 Z= 0.302 Chirality : 0.041 0.164 1549 Planarity : 0.004 0.036 1711 Dihedral : 4.087 25.577 1333 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 aren not related in a simple way. whole: 1.01 (0.24), residues: 1241 helix: 1.74 (0.21), residues: 629 sheet: -0.06 (0.40), residues: 170 loop : -0.55 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.011 0.001 TYR A 356 PHE 0.039 0.002 PHE A 50 TRP 0.011 0.001 TRP A 339 HIS 0.005 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9826) covalent geometry : angle 0.60780 (13334) hydrogen bonds : bond 0.04419 ( 537) hydrogen bonds : angle 4.48404 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7830 (m-10) cc_final: 0.7078 (t80) REVERT: A 51 MET cc_start: 0.4730 (tpt) cc_final: 0.4527 (tpt) REVERT: A 175 MET cc_start: 0.8151 (ttt) cc_final: 0.7487 (ttm) REVERT: A 176 MET cc_start: 0.8648 (ppp) cc_final: 0.8433 (ppp) REVERT: A 297 MET cc_start: 0.8371 (mmt) cc_final: 0.8073 (mmp) REVERT: A 682 GLU cc_start: 0.8534 (pp20) cc_final: 0.8269 (pp20) REVERT: A 709 GLN cc_start: 0.8891 (pp30) cc_final: 0.8373 (pp30) REVERT: A 710 GLU cc_start: 0.8588 (tp30) cc_final: 0.8267 (tp30) REVERT: B 124 ARG cc_start: 0.9064 (ptp-110) cc_final: 0.8833 (ptp-110) REVERT: C 39 ILE cc_start: 0.9132 (mm) cc_final: 0.8709 (tp) REVERT: C 88 LYS cc_start: 0.9369 (tppp) cc_final: 0.9025 (tppp) REVERT: C 221 ASN cc_start: 0.8891 (m-40) cc_final: 0.8556 (p0) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0902 time to fit residues: 20.1160 Evaluate side-chains 124 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 5 optimal weight: 40.0000 chunk 120 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 21 HIS B 108 ASN B 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.066409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.047238 restraints weight = 58255.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.048799 restraints weight = 36340.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.049848 restraints weight = 26005.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.050557 restraints weight = 20622.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.050957 restraints weight = 17578.559| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9826 Z= 0.126 Angle : 0.610 8.219 13334 Z= 0.302 Chirality : 0.041 0.186 1549 Planarity : 0.004 0.035 1711 Dihedral : 4.070 25.118 1333 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 aren not related in a simple way. whole: 1.02 (0.24), residues: 1241 helix: 1.75 (0.21), residues: 629 sheet: -0.08 (0.40), residues: 170 loop : -0.52 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.004 0.001 TYR A 356 PHE 0.072 0.002 PHE A 50 TRP 0.012 0.001 TRP A 339 HIS 0.006 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9826) covalent geometry : angle 0.61007 (13334) hydrogen bonds : bond 0.04344 ( 537) hydrogen bonds : angle 4.36488 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7948 (m-80) cc_final: 0.6486 (t80) REVERT: A 51 MET cc_start: 0.4577 (tpt) cc_final: 0.4161 (tpt) REVERT: A 175 MET cc_start: 0.8117 (ttt) cc_final: 0.7432 (ttm) REVERT: A 297 MET cc_start: 0.8333 (mmt) cc_final: 0.8041 (mmp) REVERT: A 709 GLN cc_start: 0.8876 (pp30) cc_final: 0.8518 (tm-30) REVERT: B 110 GLU cc_start: 0.8786 (tt0) cc_final: 0.8245 (tt0) REVERT: B 138 LYS cc_start: 0.8738 (pttp) cc_final: 0.8482 (ptmt) REVERT: C 39 ILE cc_start: 0.9100 (mm) cc_final: 0.8684 (tp) REVERT: C 61 ASP cc_start: 0.8736 (t0) cc_final: 0.8506 (t0) REVERT: C 88 LYS cc_start: 0.9344 (tppp) cc_final: 0.9009 (tppp) REVERT: C 179 ARG cc_start: 0.8513 (tpt90) cc_final: 0.7999 (tpm170) REVERT: C 183 ASP cc_start: 0.8878 (p0) cc_final: 0.7534 (p0) REVERT: C 221 ASN cc_start: 0.8903 (m-40) cc_final: 0.8586 (p0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0937 time to fit residues: 21.4387 Evaluate side-chains 125 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 0.0010 chunk 63 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 21 HIS B 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.066391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047257 restraints weight = 58268.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.048792 restraints weight = 36305.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.049806 restraints weight = 26111.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.050537 restraints weight = 20792.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.050975 restraints weight = 17727.722| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9826 Z= 0.129 Angle : 0.612 9.856 13334 Z= 0.300 Chirality : 0.041 0.172 1549 Planarity : 0.004 0.038 1711 Dihedral : 4.042 25.080 1333 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 aren not related in a simple way. whole: 1.11 (0.24), residues: 1241 helix: 1.81 (0.20), residues: 629 sheet: -0.05 (0.40), residues: 170 loop : -0.45 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.010 0.001 TYR A 356 PHE 0.055 0.002 PHE A 50 TRP 0.011 0.001 TRP A 339 HIS 0.006 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9826) covalent geometry : angle 0.61194 (13334) hydrogen bonds : bond 0.04305 ( 537) hydrogen bonds : angle 4.32629 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7933 (m-80) cc_final: 0.6415 (t80) REVERT: A 51 MET cc_start: 0.4538 (tpt) cc_final: 0.4276 (tpt) REVERT: A 175 MET cc_start: 0.8126 (ttt) cc_final: 0.7225 (ttt) REVERT: A 297 MET cc_start: 0.8291 (mmt) cc_final: 0.8007 (mmp) REVERT: A 709 GLN cc_start: 0.8888 (pp30) cc_final: 0.8405 (pp30) REVERT: A 710 GLU cc_start: 0.8527 (tp30) cc_final: 0.8244 (tp30) REVERT: B 110 GLU cc_start: 0.8766 (tt0) cc_final: 0.8310 (tt0) REVERT: B 138 LYS cc_start: 0.8718 (pttp) cc_final: 0.8488 (ptmt) REVERT: C 13 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9067 (mmmm) REVERT: C 39 ILE cc_start: 0.9091 (mm) cc_final: 0.8667 (tp) REVERT: C 88 LYS cc_start: 0.9344 (tppp) cc_final: 0.9036 (tppp) REVERT: C 179 ARG cc_start: 0.8527 (tpt90) cc_final: 0.7994 (tpm170) REVERT: C 183 ASP cc_start: 0.8877 (p0) cc_final: 0.7540 (p0) REVERT: C 221 ASN cc_start: 0.8906 (m-40) cc_final: 0.8655 (p0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.0888 time to fit residues: 20.5447 Evaluate side-chains 131 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 0.0970 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 21 HIS B 108 ASN B 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.066695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047636 restraints weight = 57967.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.049173 restraints weight = 36225.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.050251 restraints weight = 26016.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.050975 restraints weight = 20563.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.051432 restraints weight = 17462.764| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9826 Z= 0.120 Angle : 0.623 9.528 13334 Z= 0.303 Chirality : 0.041 0.176 1549 Planarity : 0.004 0.039 1711 Dihedral : 4.043 24.519 1333 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 aren not related in a simple way. whole: 1.12 (0.24), residues: 1241 helix: 1.83 (0.20), residues: 629 sheet: -0.04 (0.40), residues: 170 loop : -0.48 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.008 0.001 TYR A 356 PHE 0.051 0.001 PHE A 50 TRP 0.012 0.001 TRP A 339 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9826) covalent geometry : angle 0.62295 (13334) hydrogen bonds : bond 0.04265 ( 537) hydrogen bonds : angle 4.34094 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7830 (m-80) cc_final: 0.6286 (t80) REVERT: A 51 MET cc_start: 0.4332 (tpt) cc_final: 0.4026 (tpt) REVERT: A 175 MET cc_start: 0.8116 (ttt) cc_final: 0.7203 (ttt) REVERT: A 176 MET cc_start: 0.8522 (ppp) cc_final: 0.8312 (ppp) REVERT: A 297 MET cc_start: 0.8232 (mmt) cc_final: 0.7958 (mmp) REVERT: A 301 LEU cc_start: 0.9375 (tp) cc_final: 0.9163 (tp) REVERT: A 704 MET cc_start: 0.8485 (mmp) cc_final: 0.8227 (mmm) REVERT: A 709 GLN cc_start: 0.8843 (pp30) cc_final: 0.8427 (tm-30) REVERT: B 110 GLU cc_start: 0.8763 (tt0) cc_final: 0.8294 (tt0) REVERT: B 138 LYS cc_start: 0.8678 (pttp) cc_final: 0.8456 (ptmt) REVERT: C 39 ILE cc_start: 0.9031 (mm) cc_final: 0.8610 (tp) REVERT: C 88 LYS cc_start: 0.9297 (tppp) cc_final: 0.9009 (tppp) REVERT: C 179 ARG cc_start: 0.8480 (tpt90) cc_final: 0.7988 (tpm170) REVERT: C 183 ASP cc_start: 0.8844 (p0) cc_final: 0.7484 (p0) REVERT: C 221 ASN cc_start: 0.8857 (m-40) cc_final: 0.8625 (p0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0906 time to fit residues: 21.1272 Evaluate side-chains 130 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 21 HIS B 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.066203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047158 restraints weight = 58435.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.048707 restraints weight = 36456.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.049775 restraints weight = 26199.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.050443 restraints weight = 20748.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.050929 restraints weight = 17735.255| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9826 Z= 0.142 Angle : 0.622 9.111 13334 Z= 0.306 Chirality : 0.041 0.183 1549 Planarity : 0.004 0.041 1711 Dihedral : 4.047 24.988 1333 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 aren not related in a simple way. whole: 1.14 (0.24), residues: 1241 helix: 1.83 (0.21), residues: 629 sheet: -0.03 (0.40), residues: 170 loop : -0.45 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.007 0.001 TYR A 356 PHE 0.056 0.002 PHE A 50 TRP 0.010 0.001 TRP A 339 HIS 0.005 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9826) covalent geometry : angle 0.62224 (13334) hydrogen bonds : bond 0.04333 ( 537) hydrogen bonds : angle 4.36163 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7858 (m-80) cc_final: 0.6351 (t80) REVERT: A 51 MET cc_start: 0.4416 (tpt) cc_final: 0.4186 (tpt) REVERT: A 175 MET cc_start: 0.8174 (ttt) cc_final: 0.7521 (ttm) REVERT: A 254 LEU cc_start: 0.9575 (mm) cc_final: 0.9316 (tp) REVERT: A 297 MET cc_start: 0.8267 (mmt) cc_final: 0.7988 (mmp) REVERT: A 647 MET cc_start: 0.6631 (ppp) cc_final: 0.6428 (ppp) REVERT: A 704 MET cc_start: 0.8481 (mmp) cc_final: 0.8181 (mmm) REVERT: A 709 GLN cc_start: 0.8878 (pp30) cc_final: 0.8386 (pp30) REVERT: A 710 GLU cc_start: 0.8462 (tp30) cc_final: 0.8214 (tp30) REVERT: B 110 GLU cc_start: 0.8765 (tt0) cc_final: 0.8291 (tt0) REVERT: B 138 LYS cc_start: 0.8636 (pttp) cc_final: 0.8427 (ptmt) REVERT: C 13 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8764 (mmmm) REVERT: C 39 ILE cc_start: 0.9035 (mm) cc_final: 0.8627 (tp) REVERT: C 88 LYS cc_start: 0.9342 (tppp) cc_final: 0.9038 (tppp) REVERT: C 179 ARG cc_start: 0.8494 (tpt90) cc_final: 0.8009 (tpm170) REVERT: C 183 ASP cc_start: 0.8841 (p0) cc_final: 0.7493 (p0) REVERT: C 221 ASN cc_start: 0.8908 (m-40) cc_final: 0.8675 (p0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0927 time to fit residues: 21.4064 Evaluate side-chains 134 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 21 HIS B 108 ASN B 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.063530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044541 restraints weight = 59717.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045962 restraints weight = 37780.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046965 restraints weight = 27493.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.047640 restraints weight = 22005.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.048006 restraints weight = 18865.474| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9826 Z= 0.235 Angle : 0.716 8.650 13334 Z= 0.353 Chirality : 0.043 0.194 1549 Planarity : 0.004 0.049 1711 Dihedral : 4.319 26.909 1333 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 aren not related in a simple way. whole: 0.83 (0.24), residues: 1241 helix: 1.56 (0.20), residues: 634 sheet: -0.19 (0.40), residues: 181 loop : -0.58 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 653 TYR 0.008 0.002 TYR A 106 PHE 0.052 0.002 PHE A 50 TRP 0.012 0.002 TRP A 423 HIS 0.008 0.002 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 9826) covalent geometry : angle 0.71610 (13334) hydrogen bonds : bond 0.04721 ( 537) hydrogen bonds : angle 4.62903 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.04 seconds wall clock time: 35 minutes 15.53 seconds (2115.53 seconds total)