Starting phenix.real_space_refine on Tue Jan 14 04:37:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cx3_45977/01_2025/9cx3_45977.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cx3_45977/01_2025/9cx3_45977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cx3_45977/01_2025/9cx3_45977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cx3_45977/01_2025/9cx3_45977.map" model { file = "/net/cci-nas-00/data/ceres_data/9cx3_45977/01_2025/9cx3_45977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cx3_45977/01_2025/9cx3_45977.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.048 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 6 5.49 5 S 16 5.16 5 C 3560 2.51 5 N 946 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5626 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 843 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 439 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 120 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2565 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 301} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Time building chain proxies: 3.97, per 1000 atoms: 0.71 Number of scatterers: 5626 At special positions: 0 Unit cell: (60.8256, 123.034, 109.21, 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 16 16.00 P 6 15.00 O 1098 8.00 N 946 7.00 C 3560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS B 120 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 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: 1.41 Conformation dependent library (CDL) restraints added in 643.6 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 5.8% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.710A pdb=" N TYR C 136 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.796A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.083A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.541A pdb=" N ASN B 162 " --> pdb=" O HIS B 159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.082A pdb=" N THR A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 68 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.600A pdb=" N THR A 111 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET A 34 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'C' and resid 119 through 122 Processing sheet with id=AA5, first strand: chain 'H' and resid 9 through 10 removed outlier: 3.684A pdb=" N MET H 86 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 9 through 10 removed outlier: 3.929A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 61 through 63 removed outlier: 5.131A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR H 97 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 117 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 361 through 364 removed outlier: 3.866A pdb=" N VAL B 40 " --> pdb=" O TYR B 21 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.513A pdb=" N ALA B 148 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AB2, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.617A pdb=" N LEU B 274 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 272 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.543A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 235 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'L' and resid 20 through 23 removed outlier: 3.777A pdb=" N THR L 73 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.649A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN L 39 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 173 hydrogen bonds defined for protein. 447 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: 1.63 Time building geometry restraints manager: 1.63 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: 1791 1.34 - 1.46: 1266 1.46 - 1.58: 2649 1.58 - 1.70: 15 1.70 - 1.81: 23 Bond restraints: 5744 Sorted by residual: bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.614 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.717 1.614 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O2P SEP V 357 " pdb=" P SEP V 357 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" O3P SEP V 357 " pdb=" P SEP V 357 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" O1P SEP V 357 " pdb=" P SEP V 357 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 5739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 7624 2.07 - 4.13: 160 4.13 - 6.20: 12 6.20 - 8.26: 3 8.26 - 10.33: 4 Bond angle restraints: 7803 Sorted by residual: angle pdb=" C PHE H 105 " pdb=" CA PHE H 105 " pdb=" CB PHE H 105 " ideal model delta sigma weight residual 110.14 116.42 -6.28 1.60e+00 3.91e-01 1.54e+01 angle pdb=" CB MET B 192 " pdb=" CG MET B 192 " pdb=" SD MET B 192 " ideal model delta sigma weight residual 112.70 123.03 -10.33 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CA SER B 265 " pdb=" C SER B 265 " pdb=" O SER B 265 " ideal model delta sigma weight residual 121.65 117.89 3.76 1.17e+00 7.31e-01 1.03e+01 angle pdb=" CA LEU B 315 " pdb=" C LEU B 315 " pdb=" O LEU B 315 " ideal model delta sigma weight residual 121.28 117.53 3.75 1.18e+00 7.18e-01 1.01e+01 angle pdb=" CA ARG H 103 " pdb=" C ARG H 103 " pdb=" O ARG H 103 " ideal model delta sigma weight residual 120.92 117.43 3.49 1.14e+00 7.69e-01 9.39e+00 ... (remaining 7798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 3015 17.41 - 34.83: 302 34.83 - 52.24: 77 52.24 - 69.65: 19 69.65 - 87.07: 7 Dihedral angle restraints: 3420 sinusoidal: 1330 harmonic: 2090 Sorted by residual: dihedral pdb=" CA PHE A 29 " pdb=" C PHE A 29 " pdb=" N ASP A 30 " pdb=" CA ASP A 30 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU H 89 " pdb=" C LEU H 89 " pdb=" N ARG H 90 " pdb=" CA ARG H 90 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASN B 222 " pdb=" C ASN B 222 " pdb=" N ASN B 223 " pdb=" CA ASN B 223 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 703 0.048 - 0.096: 127 0.096 - 0.144: 46 0.144 - 0.192: 4 0.192 - 0.239: 2 Chirality restraints: 882 Sorted by residual: chirality pdb=" CA VAL B 262 " pdb=" N VAL B 262 " pdb=" C VAL B 262 " pdb=" CB VAL B 262 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE B 317 " pdb=" N ILE B 317 " pdb=" C ILE B 317 " pdb=" CB ILE B 317 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB TPO V 359 " pdb=" CA TPO V 359 " pdb=" OG1 TPO V 359 " pdb=" CG2 TPO V 359 " both_signs ideal model delta sigma weight residual False 2.48 2.64 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 879 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 106 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" CD GLU C 106 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU C 106 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU C 106 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA H 43 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO H 44 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 44 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 44 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 113 " 0.011 2.00e-02 2.50e+03 1.08e-02 2.90e+00 pdb=" CG TRP H 113 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP H 113 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP H 113 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 113 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 113 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 113 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 113 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 113 " 0.001 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 506 2.74 - 3.28: 5405 3.28 - 3.82: 8709 3.82 - 4.36: 10005 4.36 - 4.90: 17963 Nonbonded interactions: 42588 Sorted by model distance: nonbonded pdb=" OE2 GLU H 9 " pdb=" OG1 THR H 117 " model vdw 2.201 3.040 nonbonded pdb=" NE1 TRP H 50 " pdb=" OG SER H 53 " model vdw 2.249 3.120 nonbonded pdb=" O TYR H 58 " pdb=" NH2 ARG B 282 " model vdw 2.285 3.120 nonbonded pdb=" O LEU B 123 " pdb=" NZ LYS B 170 " model vdw 2.287 3.120 nonbonded pdb=" NZ LYS B 11 " pdb=" O ARG B 165 " model vdw 2.289 3.120 ... (remaining 42583 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 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 0.103 5744 Z= 0.330 Angle : 0.709 10.330 7803 Z= 0.382 Chirality : 0.045 0.239 882 Planarity : 0.004 0.048 983 Dihedral : 15.762 87.065 2071 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.16 % Allowed : 20.20 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.31), residues: 690 helix: -0.40 (1.31), residues: 18 sheet: -0.50 (0.31), residues: 285 loop : -1.46 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 113 HIS 0.006 0.001 HIS B 210 PHE 0.020 0.002 PHE H 105 TYR 0.013 0.002 TYR C 90 ARG 0.003 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: V 358 CYS cc_start: 0.7609 (m) cc_final: 0.6726 (t) REVERT: B 59 VAL cc_start: 0.8064 (t) cc_final: 0.7836 (m) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.2269 time to fit residues: 28.9789 Evaluate side-chains 88 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.184616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169591 restraints weight = 9234.015| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.89 r_work: 0.3967 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5744 Z= 0.224 Angle : 0.620 7.321 7803 Z= 0.324 Chirality : 0.043 0.154 882 Planarity : 0.004 0.046 983 Dihedral : 6.268 60.738 797 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.28 % Allowed : 20.20 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.31), residues: 690 helix: -0.42 (1.34), residues: 18 sheet: -0.33 (0.30), residues: 282 loop : -1.54 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 106 HIS 0.004 0.001 HIS B 198 PHE 0.030 0.002 PHE H 105 TYR 0.018 0.002 TYR H 97 ARG 0.003 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.644 Fit side-chains REVERT: A 76 ASN cc_start: 0.7225 (m-40) cc_final: 0.6989 (t0) REVERT: H 113 TRP cc_start: 0.3657 (m100) cc_final: 0.2594 (m100) REVERT: B 295 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7395 (t-90) outliers start: 20 outliers final: 9 residues processed: 112 average time/residue: 0.2009 time to fit residues: 28.7213 Evaluate side-chains 95 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain L residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 58 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS ** B 281 ASN ** 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 = 0.4188 r_free = 0.4188 target = 0.181938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.166961 restraints weight = 9288.451| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.88 r_work: 0.3929 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5744 Z= 0.282 Angle : 0.643 7.999 7803 Z= 0.337 Chirality : 0.044 0.144 882 Planarity : 0.004 0.045 983 Dihedral : 6.322 58.988 797 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.60 % Allowed : 20.03 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.31), residues: 690 helix: -0.83 (1.17), residues: 23 sheet: -0.32 (0.30), residues: 277 loop : -1.65 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 106 HIS 0.011 0.001 HIS C 122 PHE 0.037 0.002 PHE H 105 TYR 0.022 0.002 TYR H 97 ARG 0.005 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5111 (OUTLIER) cc_final: 0.3512 (t80) REVERT: B 18 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7243 (tp) REVERT: B 188 ARG cc_start: 0.7606 (tpp-160) cc_final: 0.7213 (tpm170) REVERT: B 192 MET cc_start: 0.7831 (tmm) cc_final: 0.7602 (tmm) REVERT: B 295 HIS cc_start: 0.7682 (OUTLIER) cc_final: 0.7349 (t-90) outliers start: 28 outliers final: 15 residues processed: 108 average time/residue: 0.2013 time to fit residues: 27.5863 Evaluate side-chains 106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.0570 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.182949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.167780 restraints weight = 9408.683| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.91 r_work: 0.3938 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5744 Z= 0.224 Angle : 0.608 7.534 7803 Z= 0.317 Chirality : 0.043 0.142 882 Planarity : 0.004 0.045 983 Dihedral : 6.309 63.054 797 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.25 % Allowed : 20.53 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.31), residues: 690 helix: -0.56 (1.24), residues: 23 sheet: -0.36 (0.31), residues: 283 loop : -1.55 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 106 HIS 0.008 0.001 HIS C 122 PHE 0.029 0.002 PHE H 105 TYR 0.026 0.002 TYR B 63 ARG 0.004 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.5280 (tmtt) cc_final: 0.5058 (tptp) REVERT: B 18 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7123 (tp) REVERT: B 295 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7278 (t-90) outliers start: 32 outliers final: 16 residues processed: 115 average time/residue: 0.1978 time to fit residues: 28.8110 Evaluate side-chains 101 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 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 = 0.4152 r_free = 0.4152 target = 0.178274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.163148 restraints weight = 9363.090| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.86 r_work: 0.3889 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 5744 Z= 0.400 Angle : 0.734 8.375 7803 Z= 0.384 Chirality : 0.047 0.162 882 Planarity : 0.005 0.044 983 Dihedral : 6.734 55.362 797 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 7.22 % Allowed : 20.36 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.31), residues: 690 helix: 0.79 (1.43), residues: 17 sheet: -0.59 (0.30), residues: 282 loop : -1.70 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP H 50 HIS 0.008 0.002 HIS C 122 PHE 0.052 0.003 PHE H 105 TYR 0.033 0.003 TYR B 63 ARG 0.009 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 0.645 Fit side-chains REVERT: A 82 MET cc_start: 0.7411 (mmm) cc_final: 0.6486 (mmm) REVERT: B 188 ARG cc_start: 0.7686 (tpm170) cc_final: 0.7347 (tpm170) REVERT: B 317 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7802 (mt) REVERT: L 3 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.6974 (tp) outliers start: 44 outliers final: 30 residues processed: 118 average time/residue: 0.1933 time to fit residues: 29.3555 Evaluate side-chains 113 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain V residue 358 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.179058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.164117 restraints weight = 9190.217| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.84 r_work: 0.3901 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5744 Z= 0.320 Angle : 0.676 7.702 7803 Z= 0.354 Chirality : 0.045 0.143 882 Planarity : 0.004 0.044 983 Dihedral : 6.719 60.531 797 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 7.88 % Allowed : 20.85 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.31), residues: 690 helix: 0.76 (1.42), residues: 17 sheet: -0.79 (0.30), residues: 290 loop : -1.73 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 106 HIS 0.003 0.001 HIS B 210 PHE 0.050 0.003 PHE H 105 TYR 0.026 0.002 TYR B 63 ARG 0.007 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5404 (OUTLIER) cc_final: 0.4669 (t80) REVERT: A 82 MET cc_start: 0.7492 (mmm) cc_final: 0.5699 (tpt) REVERT: C 128 GLN cc_start: 0.7051 (mp10) cc_final: 0.6845 (mp10) REVERT: B 188 ARG cc_start: 0.7650 (tpm170) cc_final: 0.7355 (tpm170) REVERT: B 240 ASP cc_start: 0.6561 (p0) cc_final: 0.6340 (p0) REVERT: B 295 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7297 (t-90) REVERT: B 317 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7789 (mt) REVERT: L 3 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.6945 (tp) outliers start: 48 outliers final: 36 residues processed: 122 average time/residue: 0.1930 time to fit residues: 30.1943 Evaluate side-chains 121 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain V residue 358 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.0270 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.180716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.165940 restraints weight = 9307.511| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.87 r_work: 0.3937 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5744 Z= 0.214 Angle : 0.619 7.429 7803 Z= 0.320 Chirality : 0.043 0.140 882 Planarity : 0.004 0.043 983 Dihedral : 6.506 67.659 797 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 6.57 % Allowed : 22.66 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.32), residues: 690 helix: 1.07 (1.48), residues: 17 sheet: -0.69 (0.30), residues: 291 loop : -1.62 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.004 0.001 HIS B 210 PHE 0.037 0.002 PHE H 105 TYR 0.024 0.002 TYR B 63 ARG 0.004 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7418 (ttm110) cc_final: 0.7037 (mtp180) REVERT: A 67 PHE cc_start: 0.5083 (OUTLIER) cc_final: 0.4122 (t80) REVERT: A 82 MET cc_start: 0.7414 (mmm) cc_final: 0.7181 (mmm) REVERT: B 188 ARG cc_start: 0.7594 (tpm170) cc_final: 0.7349 (tpm170) REVERT: B 240 ASP cc_start: 0.6506 (p0) cc_final: 0.6250 (p0) REVERT: B 295 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.7294 (t-90) REVERT: B 317 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7842 (mp) REVERT: L 3 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.6890 (tp) outliers start: 40 outliers final: 29 residues processed: 113 average time/residue: 0.1866 time to fit residues: 27.3338 Evaluate side-chains 114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain V residue 358 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.0070 chunk 23 optimal weight: 0.4980 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 0.0470 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 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 = 0.4213 r_free = 0.4213 target = 0.183779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169190 restraints weight = 9205.569| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.86 r_work: 0.3963 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5744 Z= 0.177 Angle : 0.591 7.680 7803 Z= 0.304 Chirality : 0.042 0.139 882 Planarity : 0.004 0.043 983 Dihedral : 6.281 72.808 797 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.25 % Allowed : 23.48 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.32), residues: 690 helix: 1.30 (1.53), residues: 17 sheet: -0.62 (0.30), residues: 288 loop : -1.57 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 113 HIS 0.004 0.001 HIS B 210 PHE 0.024 0.002 PHE H 105 TYR 0.021 0.001 TYR B 63 ARG 0.003 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7354 (ttm110) cc_final: 0.6997 (mtp180) REVERT: A 67 PHE cc_start: 0.4978 (OUTLIER) cc_final: 0.4049 (t80) REVERT: A 82 MET cc_start: 0.7406 (mmm) cc_final: 0.6804 (mmm) REVERT: H 113 TRP cc_start: 0.3808 (m100) cc_final: 0.2756 (m100) REVERT: B 240 ASP cc_start: 0.6403 (p0) cc_final: 0.6109 (p0) REVERT: B 295 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7262 (t-90) REVERT: L 5 MET cc_start: 0.4448 (mtp) cc_final: 0.4238 (mtp) outliers start: 32 outliers final: 23 residues processed: 109 average time/residue: 0.2099 time to fit residues: 29.1243 Evaluate side-chains 107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.0030 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.164786 restraints weight = 9182.596| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.87 r_work: 0.3922 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5744 Z= 0.280 Angle : 0.657 7.706 7803 Z= 0.342 Chirality : 0.044 0.150 882 Planarity : 0.004 0.043 983 Dihedral : 6.397 66.793 797 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.25 % Allowed : 22.66 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.32), residues: 690 helix: 1.09 (1.48), residues: 17 sheet: -0.66 (0.30), residues: 279 loop : -1.54 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 113 HIS 0.006 0.001 HIS C 122 PHE 0.020 0.002 PHE H 105 TYR 0.022 0.002 TYR B 63 ARG 0.008 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7093 (mtp180) REVERT: A 67 PHE cc_start: 0.5328 (OUTLIER) cc_final: 0.4312 (t80) REVERT: A 82 MET cc_start: 0.7328 (mmm) cc_final: 0.6693 (mmm) REVERT: H 53 SER cc_start: 0.7221 (t) cc_final: 0.6993 (m) REVERT: B 188 ARG cc_start: 0.7566 (tpm170) cc_final: 0.7315 (tpm170) REVERT: B 295 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.7322 (t-90) outliers start: 32 outliers final: 27 residues processed: 111 average time/residue: 0.1854 time to fit residues: 26.6707 Evaluate side-chains 114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain V residue 358 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.178810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163933 restraints weight = 9446.220| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.89 r_work: 0.3904 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5744 Z= 0.328 Angle : 0.697 8.267 7803 Z= 0.363 Chirality : 0.045 0.167 882 Planarity : 0.005 0.042 983 Dihedral : 6.617 64.906 797 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.93 % Allowed : 23.48 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.31), residues: 690 helix: 1.04 (1.49), residues: 17 sheet: -0.76 (0.30), residues: 279 loop : -1.64 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP H 113 HIS 0.004 0.001 HIS C 122 PHE 0.021 0.002 PHE H 105 TYR 0.021 0.002 TYR B 63 ARG 0.009 0.001 ARG A 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.495 Fit side-chains REVERT: A 19 ARG cc_start: 0.7569 (ttm110) cc_final: 0.6978 (mtp180) REVERT: A 67 PHE cc_start: 0.5799 (OUTLIER) cc_final: 0.4557 (t80) REVERT: A 82 MET cc_start: 0.7348 (mmm) cc_final: 0.7112 (mmm) REVERT: B 295 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7311 (t-90) outliers start: 30 outliers final: 28 residues processed: 112 average time/residue: 0.1876 time to fit residues: 26.9556 Evaluate side-chains 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain V residue 358 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 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 = 0.4170 r_free = 0.4170 target = 0.179472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.164686 restraints weight = 9350.273| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.88 r_work: 0.3913 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5744 Z= 0.279 Angle : 0.678 8.273 7803 Z= 0.353 Chirality : 0.045 0.151 882 Planarity : 0.004 0.042 983 Dihedral : 6.624 67.732 797 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.91 % Allowed : 23.15 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.31), residues: 690 helix: 0.98 (1.46), residues: 17 sheet: -0.80 (0.30), residues: 279 loop : -1.66 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 113 HIS 0.003 0.001 HIS C 122 PHE 0.018 0.002 PHE H 105 TYR 0.021 0.002 TYR A 94 ARG 0.008 0.001 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.14 seconds wall clock time: 55 minutes 41.98 seconds (3341.98 seconds total)