Starting phenix.real_space_refine on Thu Jun 5 07:30:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cx3_45977/06_2025/9cx3_45977.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cx3_45977/06_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_45977/06_2025/9cx3_45977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cx3_45977/06_2025/9cx3_45977.map" model { file = "/net/cci-nas-00/data/ceres_data/9cx3_45977/06_2025/9cx3_45977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cx3_45977/06_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-5710/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: 5.76, per 1000 atoms: 1.02 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: 1.29 Conformation dependent library (CDL) restraints added in 610.1 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: 0.89 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: 4.74 Time building geometry restraints manager: 1.54 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: 43.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 23.060 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:3.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.610 ------------------------------------------------------------------------------- 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 5747 Z= 0.252 Angle : 0.709 10.330 7809 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 Details of bonding type rmsd hydrogen bonds : bond 0.25800 ( 169) hydrogen bonds : angle 10.60260 ( 447) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.46877 ( 6) covalent geometry : bond 0.00479 ( 5744) covalent geometry : angle 0.70930 ( 7803) *********************** 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 : 0.651 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: 0.2331 time to fit residues: 29.9469 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 : 0.602 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169590 restraints weight = 9234.024| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.89 r_work: 0.3971 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 5747 Z= 0.156 Angle : 0.621 7.321 7809 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 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 169) hydrogen bonds : angle 7.34881 ( 447) SS BOND : bond 0.00227 ( 3) SS BOND : angle 1.10936 ( 6) covalent geometry : bond 0.00347 ( 5744) covalent geometry : angle 0.62049 ( 7803) *********************** 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 : 0.617 Fit side-chains REVERT: A 76 ASN cc_start: 0.7240 (m-40) cc_final: 0.6998 (t0) REVERT: H 113 TRP cc_start: 0.3656 (m100) cc_final: 0.2590 (m100) REVERT: B 295 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7406 (t-90) outliers start: 20 outliers final: 9 residues processed: 112 average time/residue: 0.2285 time to fit residues: 32.8259 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 : 0.710 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.0670 chunk 58 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.182775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.167711 restraints weight = 9278.005| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.90 r_work: 0.3937 rms_B_bonded: 2.62 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: 0.6967 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5747 Z= 0.175 Angle : 0.630 8.003 7809 Z= 0.329 Chirality : 0.043 0.144 882 Planarity : 0.004 0.045 983 Dihedral : 6.261 60.034 797 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.27 % Allowed : 20.53 % Favored : 75.21 % 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: -0.80 (1.17), residues: 23 sheet: -0.28 (0.30), residues: 277 loop : -1.63 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.007 0.001 HIS C 122 PHE 0.034 0.002 PHE H 105 TYR 0.022 0.002 TYR H 97 ARG 0.004 0.001 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 169) hydrogen bonds : angle 6.93569 ( 447) SS BOND : bond 0.00339 ( 3) SS BOND : angle 1.06102 ( 6) covalent geometry : bond 0.00401 ( 5744) covalent geometry : angle 0.62915 ( 7803) *********************** 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 113 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.3358 (t80) REVERT: B 18 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7198 (tp) REVERT: B 188 ARG cc_start: 0.7599 (tpp-160) cc_final: 0.7216 (tpm170) REVERT: B 192 MET cc_start: 0.7788 (tmm) cc_final: 0.7553 (tmm) REVERT: B 295 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7330 (t-90) outliers start: 26 outliers final: 13 residues processed: 108 average time/residue: 0.2010 time to fit residues: 27.8375 Evaluate side-chains 104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 C residue 122 HIS Chi-restraints excluded: chain H residue 8 VAL 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: 0.5980 chunk 14 optimal weight: 0.0010 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 0.0040 overall best weight: 0.2396 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.185192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.169873 restraints weight = 9385.070| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.94 r_work: 0.3959 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5747 Z= 0.121 Angle : 0.581 7.500 7809 Z= 0.301 Chirality : 0.042 0.143 882 Planarity : 0.004 0.045 983 Dihedral : 6.163 65.236 797 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.27 % Allowed : 21.51 % 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: -1.39 (0.31), residues: 690 helix: -0.44 (1.26), residues: 23 sheet: -0.23 (0.31), residues: 280 loop : -1.50 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 106 HIS 0.009 0.001 HIS C 122 PHE 0.024 0.001 PHE H 105 TYR 0.025 0.001 TYR B 63 ARG 0.002 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 169) hydrogen bonds : angle 6.40566 ( 447) SS BOND : bond 0.00322 ( 3) SS BOND : angle 0.82662 ( 6) covalent geometry : bond 0.00271 ( 5744) covalent geometry : angle 0.58106 ( 7803) *********************** 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 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.5289 (tmtt) cc_final: 0.5087 (tptp) REVERT: B 18 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7089 (tp) REVERT: B 295 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.7292 (t-90) outliers start: 26 outliers final: 12 residues processed: 113 average time/residue: 0.1949 time to fit residues: 28.4378 Evaluate side-chains 96 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 H residue 106 TRP 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 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 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: 0.9980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0030 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 = 0.180048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.164730 restraints weight = 9345.721| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.90 r_work: 0.3903 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 5747 Z= 0.238 Angle : 0.685 8.565 7809 Z= 0.357 Chirality : 0.045 0.159 882 Planarity : 0.004 0.043 983 Dihedral : 6.452 57.314 797 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.42 % Allowed : 20.53 % Favored : 74.06 % 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: -1.56 (0.31), residues: 690 helix: 1.03 (1.48), residues: 17 sheet: -0.46 (0.31), residues: 285 loop : -1.60 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 106 HIS 0.006 0.001 HIS C 122 PHE 0.049 0.003 PHE H 105 TYR 0.033 0.002 TYR B 63 ARG 0.008 0.001 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 169) hydrogen bonds : angle 6.83441 ( 447) SS BOND : bond 0.00395 ( 3) SS BOND : angle 1.00899 ( 6) covalent geometry : bond 0.00547 ( 5744) covalent geometry : angle 0.68442 ( 7803) *********************** 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 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7082 (mtp180) REVERT: A 67 PHE cc_start: 0.4619 (OUTLIER) cc_final: 0.3931 (t80) REVERT: B 188 ARG cc_start: 0.7654 (tpm170) cc_final: 0.7276 (tpm170) REVERT: B 295 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7361 (t-90) REVERT: L 3 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.6934 (tp) outliers start: 33 outliers final: 22 residues processed: 108 average time/residue: 0.2083 time to fit residues: 28.5717 Evaluate side-chains 105 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 B residue 6 THR Chi-restraints excluded: chain B residue 58 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 289 LEU 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 3 ILE Chi-restraints excluded: chain L residue 6 THR 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: 0.7980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.183134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.168398 restraints weight = 9187.112| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 1.85 r_work: 0.3951 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5747 Z= 0.136 Angle : 0.597 7.585 7809 Z= 0.308 Chirality : 0.043 0.140 882 Planarity : 0.004 0.042 983 Dihedral : 6.300 67.359 797 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.25 % Allowed : 22.00 % Favored : 72.74 % 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: -1.48 (0.31), residues: 690 helix: 1.25 (1.52), residues: 17 sheet: -0.37 (0.30), residues: 290 loop : -1.60 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 106 HIS 0.002 0.001 HIS C 122 PHE 0.032 0.002 PHE H 105 TYR 0.027 0.002 TYR B 63 ARG 0.004 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 169) hydrogen bonds : angle 6.29057 ( 447) SS BOND : bond 0.00344 ( 3) SS BOND : angle 0.70191 ( 6) covalent geometry : bond 0.00309 ( 5744) covalent geometry : angle 0.59654 ( 7803) *********************** 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 117 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 128 GLN cc_start: 0.6935 (mp10) cc_final: 0.6714 (mp10) REVERT: B 188 ARG cc_start: 0.7610 (tpm170) cc_final: 0.7355 (tpm170) REVERT: B 295 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7309 (t-90) REVERT: L 3 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.6822 (tp) outliers start: 32 outliers final: 22 residues processed: 109 average time/residue: 0.1969 time to fit residues: 27.2617 Evaluate side-chains 106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL 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 98 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 302 SER 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 75 THR 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: 0.2980 chunk 65 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.182508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.167486 restraints weight = 9309.946| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.89 r_work: 0.3941 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5747 Z= 0.154 Angle : 0.608 7.520 7809 Z= 0.315 Chirality : 0.043 0.138 882 Planarity : 0.004 0.042 983 Dihedral : 6.262 66.126 797 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.08 % Allowed : 21.51 % 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: -1.54 (0.32), residues: 690 helix: 1.22 (1.51), residues: 17 sheet: -0.47 (0.30), residues: 292 loop : -1.59 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 106 HIS 0.002 0.001 HIS C 122 PHE 0.032 0.002 PHE H 105 TYR 0.023 0.002 TYR B 63 ARG 0.005 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 169) hydrogen bonds : angle 6.30650 ( 447) SS BOND : bond 0.00316 ( 3) SS BOND : angle 0.65952 ( 6) covalent geometry : bond 0.00350 ( 5744) covalent geometry : angle 0.60836 ( 7803) *********************** 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 121 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7407 (ttm110) cc_final: 0.7067 (mtp180) REVERT: A 67 PHE cc_start: 0.4956 (OUTLIER) cc_final: 0.3854 (t80) REVERT: A 82 MET cc_start: 0.7380 (mmm) cc_final: 0.6882 (mmm) REVERT: B 188 ARG cc_start: 0.7611 (tpm170) cc_final: 0.7395 (tpm170) REVERT: B 295 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.7309 (t-90) REVERT: L 3 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.6848 (tp) outliers start: 37 outliers final: 27 residues processed: 113 average time/residue: 0.1833 time to fit residues: 26.8180 Evaluate side-chains 112 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 C residue 115 GLU 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 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 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 302 SER Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR 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: 1.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.180762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.166042 restraints weight = 9217.617| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.85 r_work: 0.3927 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5747 Z= 0.179 Angle : 0.628 7.621 7809 Z= 0.327 Chirality : 0.043 0.142 882 Planarity : 0.004 0.042 983 Dihedral : 6.334 65.607 797 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.40 % Allowed : 21.51 % 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: -1.62 (0.32), residues: 690 helix: 1.13 (1.49), residues: 17 sheet: -0.53 (0.30), residues: 292 loop : -1.64 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 106 HIS 0.004 0.001 HIS C 122 PHE 0.033 0.002 PHE H 105 TYR 0.024 0.002 TYR B 63 ARG 0.006 0.001 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 169) hydrogen bonds : angle 6.43248 ( 447) SS BOND : bond 0.00328 ( 3) SS BOND : angle 0.67392 ( 6) covalent geometry : bond 0.00409 ( 5744) covalent geometry : angle 0.62759 ( 7803) *********************** 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 126 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7396 (ttm110) cc_final: 0.7066 (mtp180) REVERT: A 67 PHE cc_start: 0.5095 (OUTLIER) cc_final: 0.4043 (t80) REVERT: A 82 MET cc_start: 0.7401 (mmm) cc_final: 0.6874 (mmm) REVERT: B 188 ARG cc_start: 0.7672 (tpm170) cc_final: 0.7471 (tpm170) REVERT: B 295 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.7279 (t-90) REVERT: L 3 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.6830 (tp) outliers start: 39 outliers final: 31 residues processed: 117 average time/residue: 0.2271 time to fit residues: 33.9782 Evaluate side-chains 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 C residue 115 GLU 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 159 HIS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 270 LYS 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 345 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 67 optimal weight: 0.0870 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.181239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.166520 restraints weight = 9214.519| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.85 r_work: 0.3934 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5747 Z= 0.169 Angle : 0.626 7.911 7809 Z= 0.326 Chirality : 0.043 0.140 882 Planarity : 0.004 0.042 983 Dihedral : 6.356 67.439 797 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 6.24 % Allowed : 22.17 % 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: -1.68 (0.32), residues: 690 helix: 1.16 (1.50), residues: 17 sheet: -0.60 (0.30), residues: 289 loop : -1.65 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 113 HIS 0.007 0.001 HIS C 122 PHE 0.032 0.002 PHE H 105 TYR 0.023 0.002 TYR B 63 ARG 0.006 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 169) hydrogen bonds : angle 6.43322 ( 447) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.65944 ( 6) covalent geometry : bond 0.00387 ( 5744) covalent geometry : angle 0.62589 ( 7803) *********************** 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 124 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7096 (mtp180) REVERT: A 67 PHE cc_start: 0.5181 (OUTLIER) cc_final: 0.4035 (t80) REVERT: A 82 MET cc_start: 0.7360 (mmm) cc_final: 0.6847 (mmm) REVERT: B 295 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.7277 (t-90) REVERT: L 3 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.6861 (tp) outliers start: 38 outliers final: 32 residues processed: 114 average time/residue: 0.3548 time to fit residues: 53.4914 Evaluate side-chains 121 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 115 GLU 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 227 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 270 LYS 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 345 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 67 optimal weight: 0.0060 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.179669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165078 restraints weight = 9433.203| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.94 r_work: 0.3920 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5747 Z= 0.189 Angle : 0.660 7.661 7809 Z= 0.343 Chirality : 0.044 0.155 882 Planarity : 0.004 0.042 983 Dihedral : 6.465 66.983 797 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 6.08 % Allowed : 22.82 % Favored : 71.10 % 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: 1.07 (1.49), residues: 17 sheet: -0.68 (0.30), residues: 282 loop : -1.62 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 113 HIS 0.004 0.001 HIS B 210 PHE 0.032 0.002 PHE H 105 TYR 0.021 0.002 TYR B 63 ARG 0.006 0.001 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 169) hydrogen bonds : angle 6.58502 ( 447) SS BOND : bond 0.00379 ( 3) SS BOND : angle 0.70901 ( 6) covalent geometry : bond 0.00434 ( 5744) covalent geometry : angle 0.66016 ( 7803) ********************** 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 125 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.667 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: 0.5294 (OUTLIER) cc_final: 0.4240 (t80) REVERT: A 82 MET cc_start: 0.7499 (mmm) cc_final: 0.6972 (tpt) REVERT: B 240 ASP cc_start: 0.6355 (p0) cc_final: 0.6144 (p0) REVERT: B 295 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7278 (t-90) REVERT: L 3 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.6894 (tp) outliers start: 37 outliers final: 30 residues processed: 114 average time/residue: 0.1835 time to fit residues: 26.7629 Evaluate side-chains 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 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 227 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 270 LYS 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 345 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.180915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166400 restraints weight = 9334.437| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.94 r_work: 0.3934 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5747 Z= 0.169 Angle : 0.658 8.012 7809 Z= 0.341 Chirality : 0.044 0.164 882 Planarity : 0.004 0.042 983 Dihedral : 6.486 69.798 797 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.75 % Allowed : 23.48 % 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: -1.74 (0.31), residues: 690 helix: 1.11 (1.50), residues: 17 sheet: -0.68 (0.31), residues: 279 loop : -1.65 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 113 HIS 0.004 0.001 HIS B 210 PHE 0.030 0.002 PHE H 105 TYR 0.022 0.002 TYR B 63 ARG 0.005 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 169) hydrogen bonds : angle 6.45310 ( 447) SS BOND : bond 0.00359 ( 3) SS BOND : angle 0.87666 ( 6) covalent geometry : bond 0.00390 ( 5744) covalent geometry : angle 0.65812 ( 7803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3551.85 seconds wall clock time: 63 minutes 11.55 seconds (3791.55 seconds total)