Starting phenix.real_space_refine on Fri Dec 27 11:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csy_26975/12_2024/8csy_26975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csy_26975/12_2024/8csy_26975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8csy_26975/12_2024/8csy_26975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csy_26975/12_2024/8csy_26975.map" model { file = "/net/cci-nas-00/data/ceres_data/8csy_26975/12_2024/8csy_26975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csy_26975/12_2024/8csy_26975.cif" } resolution = 2.7 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= 0.291 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2941 2.51 5 N 805 2.21 5 O 880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4638 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2276 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2343 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 3.62, per 1000 atoms: 0.78 Number of scatterers: 4638 At special positions: 0 Unit cell: (89.64, 83, 74.285, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 880 8.00 N 805 7.00 C 2941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 592.4 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 40.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.834A pdb=" N LYS E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 194 through 201 Processing helix chain 'E' and resid 277 through 291 Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.730A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 335 through 348 Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.532A pdb=" N HIS C 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.688A pdb=" N LYS C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 277 through 291 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.689A pdb=" N LEU C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.268A pdb=" N VAL C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 58 through 67 removed outlier: 6.017A pdb=" N GLU E 63 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU E 77 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 65 " --> pdb=" O TRP E 75 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP E 75 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP E 67 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E 73 " --> pdb=" O ASP E 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 87 current: chain 'E' and resid 262 through 270 Processing sheet with id=AA2, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 66 removed outlier: 6.584A pdb=" N VAL C 59 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 61 " --> pdb=" O ALA C 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 87 current: chain 'C' and resid 224 through 234 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 224 through 234 current: chain 'C' and resid 262 through 270 165 hydrogen bonds defined for protein. 465 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: 1.12 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1575 1.34 - 1.46: 781 1.46 - 1.57: 2337 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4713 Sorted by residual: bond pdb=" C VAL E 336 " pdb=" N PRO E 337 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.71e-01 bond pdb=" C VAL C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.336 1.346 -0.011 1.23e-02 6.61e+03 7.66e-01 bond pdb=" C PRO C 221 " pdb=" N PRO C 222 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.30e-02 5.92e+03 4.91e-01 bond pdb=" CA PRO C 271 " pdb=" C PRO C 271 " ideal model delta sigma weight residual 1.525 1.519 0.007 9.70e-03 1.06e+04 4.61e-01 bond pdb=" N ASP E 122 " pdb=" CA ASP E 122 " ideal model delta sigma weight residual 1.460 1.469 -0.010 1.42e-02 4.96e+03 4.56e-01 ... (remaining 4708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 6213 1.36 - 2.71: 155 2.71 - 4.07: 27 4.07 - 5.42: 6 5.42 - 6.78: 4 Bond angle restraints: 6405 Sorted by residual: angle pdb=" N ASN C 91 " pdb=" CA ASN C 91 " pdb=" C ASN C 91 " ideal model delta sigma weight residual 114.09 108.87 5.22 1.55e+00 4.16e-01 1.13e+01 angle pdb=" C VAL E 82 " pdb=" N GLN E 83 " pdb=" CA GLN E 83 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.06e+00 angle pdb=" N GLU C 90 " pdb=" CA GLU C 90 " pdb=" C GLU C 90 " ideal model delta sigma weight residual 111.81 108.25 3.56 1.44e+00 4.82e-01 6.10e+00 angle pdb=" N VAL E 82 " pdb=" CA VAL E 82 " pdb=" C VAL E 82 " ideal model delta sigma weight residual 109.34 104.62 4.72 2.08e+00 2.31e-01 5.15e+00 angle pdb=" CA PRO C 271 " pdb=" C PRO C 271 " pdb=" N GLU C 272 " ideal model delta sigma weight residual 114.74 116.96 -2.22 1.03e+00 9.43e-01 4.64e+00 ... (remaining 6400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 2624 16.74 - 33.47: 149 33.47 - 50.21: 70 50.21 - 66.94: 23 66.94 - 83.68: 5 Dihedral angle restraints: 2871 sinusoidal: 1175 harmonic: 1696 Sorted by residual: dihedral pdb=" CA TRP E 81 " pdb=" C TRP E 81 " pdb=" N VAL E 82 " pdb=" CA VAL E 82 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL C 57 " pdb=" C VAL C 57 " pdb=" N TYR C 58 " pdb=" CA TYR C 58 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CB GLU E 312 " pdb=" CG GLU E 312 " pdb=" CD GLU E 312 " pdb=" OE1 GLU E 312 " ideal model delta sinusoidal sigma weight residual 0.00 83.68 -83.68 1 3.00e+01 1.11e-03 9.49e+00 ... (remaining 2868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 441 0.029 - 0.057: 187 0.057 - 0.085: 71 0.085 - 0.114: 31 0.114 - 0.142: 3 Chirality restraints: 733 Sorted by residual: chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE E 220 " pdb=" N ILE E 220 " pdb=" C ILE E 220 " pdb=" CB ILE E 220 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA VAL C 82 " pdb=" N VAL C 82 " pdb=" C VAL C 82 " pdb=" CB VAL C 82 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 730 not shown) Planarity restraints: 840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 146 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO C 147 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 147 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 147 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 183 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO E 184 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 184 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 184 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 146 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO E 147 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 147 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 147 " -0.018 5.00e-02 4.00e+02 ... (remaining 837 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 688 2.76 - 3.29: 4203 3.29 - 3.83: 8186 3.83 - 4.36: 9643 4.36 - 4.90: 16030 Nonbonded interactions: 38750 Sorted by model distance: nonbonded pdb=" OG1 THR C 103 " pdb=" OG SER C 106 " model vdw 2.224 3.040 nonbonded pdb=" NH2 ARG E 292 " pdb=" O LYS E 353 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASP E 316 " pdb=" NE1 TRP C 105 " model vdw 2.305 3.120 nonbonded pdb=" O ALA E 331 " pdb=" OG SER E 334 " model vdw 2.310 3.040 nonbonded pdb=" OD2 ASP C 122 " pdb=" O HOH C1001 " model vdw 2.328 3.040 ... (remaining 38745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 56 through 203 or resid 217 through 348)) selection = (chain 'E' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348)) } 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: 1.030 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.600 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.003 0.033 4713 Z= 0.195 Angle : 0.559 6.781 6405 Z= 0.303 Chirality : 0.038 0.142 733 Planarity : 0.005 0.038 840 Dihedral : 14.356 83.678 1763 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.06 % Allowed : 8.72 % Favored : 87.22 % 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: 1.07 (0.34), residues: 574 helix: 1.13 (0.36), residues: 212 sheet: 2.27 (0.52), residues: 89 loop : -0.10 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 81 HIS 0.003 0.001 HIS E 101 PHE 0.020 0.002 PHE C 314 TYR 0.009 0.001 TYR E 278 ARG 0.003 0.000 ARG E 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 69 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.5567 (ptpt) REVERT: E 112 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7350 (ttp-170) REVERT: E 125 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7840 (mm-30) REVERT: E 233 ARG cc_start: 0.8376 (mtm180) cc_final: 0.8161 (mtm180) REVERT: E 291 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8683 (tm-30) REVERT: E 348 GLN cc_start: 0.7370 (pt0) cc_final: 0.7159 (pt0) REVERT: C 83 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: C 109 GLU cc_start: 0.7684 (tp30) cc_final: 0.7363 (mp0) REVERT: C 124 GLN cc_start: 0.8431 (mt0) cc_final: 0.7772 (tm-30) REVERT: C 198 GLN cc_start: 0.7841 (tt0) cc_final: 0.7400 (mt0) REVERT: C 300 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7721 (mmm) outliers start: 20 outliers final: 3 residues processed: 123 average time/residue: 1.5194 time to fit residues: 192.7059 Evaluate side-chains 103 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN C 144 GLN C 239 GLN C 248 GLN C 339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4713 Z= 0.303 Angle : 0.597 6.405 6405 Z= 0.301 Chirality : 0.041 0.126 733 Planarity : 0.005 0.036 840 Dihedral : 7.153 59.298 647 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.87 % Allowed : 11.97 % Favored : 83.16 % 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: 1.03 (0.34), residues: 574 helix: 1.27 (0.36), residues: 218 sheet: 2.22 (0.56), residues: 78 loop : -0.20 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 81 HIS 0.003 0.001 HIS E 309 PHE 0.023 0.002 PHE C 314 TYR 0.011 0.002 TYR E 278 ARG 0.004 0.001 ARG E 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: E 69 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5792 (ptpt) REVERT: E 112 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7348 (ttp-170) REVERT: E 116 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7955 (ptmt) REVERT: E 125 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7854 (mm-30) REVERT: E 198 GLN cc_start: 0.6780 (mt0) cc_final: 0.6358 (tp40) REVERT: E 219 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.5800 (pmtt) REVERT: E 239 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: E 348 GLN cc_start: 0.7474 (pt0) cc_final: 0.7180 (pt0) REVERT: C 83 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: C 109 GLU cc_start: 0.7638 (tp30) cc_final: 0.7161 (mm-30) REVERT: C 114 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7821 (t80) REVERT: C 124 GLN cc_start: 0.8434 (mt0) cc_final: 0.7794 (tm-30) REVERT: C 155 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7642 (ttp-110) REVERT: C 202 GLU cc_start: 0.4188 (OUTLIER) cc_final: 0.3576 (tp30) REVERT: C 233 ARG cc_start: 0.8052 (mtt-85) cc_final: 0.7777 (mpp80) REVERT: C 272 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: C 300 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7832 (mmm) REVERT: C 330 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7229 (tt0) outliers start: 24 outliers final: 7 residues processed: 103 average time/residue: 1.6064 time to fit residues: 170.5743 Evaluate side-chains 99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4713 Z= 0.217 Angle : 0.531 6.124 6405 Z= 0.269 Chirality : 0.039 0.127 733 Planarity : 0.004 0.036 840 Dihedral : 6.454 54.133 644 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.85 % Allowed : 14.40 % Favored : 81.74 % 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: 1.00 (0.34), residues: 574 helix: 1.30 (0.36), residues: 219 sheet: 2.05 (0.56), residues: 78 loop : -0.22 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS C 101 PHE 0.021 0.002 PHE C 314 TYR 0.010 0.002 TYR E 278 ARG 0.003 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: E 69 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.5787 (ptpt) REVERT: E 83 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7830 (mm-40) REVERT: E 112 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7352 (ttp-170) REVERT: E 116 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7904 (ptmt) REVERT: E 125 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7922 (mm-30) REVERT: E 158 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8374 (mm) REVERT: E 198 GLN cc_start: 0.6741 (mt0) cc_final: 0.6382 (tp40) REVERT: E 219 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.5689 (pmtt) REVERT: E 348 GLN cc_start: 0.7429 (pt0) cc_final: 0.7098 (pt0) REVERT: C 83 GLN cc_start: 0.7635 (pt0) cc_final: 0.7370 (pm20) REVERT: C 109 GLU cc_start: 0.7619 (tp30) cc_final: 0.7228 (mm-30) REVERT: C 114 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7896 (t80) REVERT: C 124 GLN cc_start: 0.8423 (mt0) cc_final: 0.7801 (tm-30) REVERT: C 202 GLU cc_start: 0.4167 (OUTLIER) cc_final: 0.3584 (tp30) REVERT: C 216 ILE cc_start: 0.5772 (OUTLIER) cc_final: 0.5391 (tp) REVERT: C 272 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: C 300 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7808 (mmm) REVERT: C 330 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7227 (tt0) outliers start: 19 outliers final: 4 residues processed: 101 average time/residue: 1.5853 time to fit residues: 165.3270 Evaluate side-chains 97 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4713 Z= 0.208 Angle : 0.520 5.772 6405 Z= 0.262 Chirality : 0.039 0.120 733 Planarity : 0.004 0.034 840 Dihedral : 6.211 53.168 641 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.07 % Allowed : 13.79 % Favored : 81.14 % 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: 1.03 (0.34), residues: 574 helix: 1.36 (0.36), residues: 219 sheet: 2.00 (0.57), residues: 78 loop : -0.22 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS C 163 PHE 0.020 0.002 PHE C 314 TYR 0.010 0.002 TYR E 278 ARG 0.004 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8956 (tt0) cc_final: 0.8708 (tt0) REVERT: E 69 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.5815 (ptpt) REVERT: E 112 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.7348 (ttp-170) REVERT: E 125 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7908 (mm-30) REVERT: E 158 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8379 (mm) REVERT: E 198 GLN cc_start: 0.6737 (mt0) cc_final: 0.6507 (tp-100) REVERT: E 219 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.5672 (pmtt) REVERT: E 348 GLN cc_start: 0.7415 (pt0) cc_final: 0.7118 (pt0) REVERT: C 83 GLN cc_start: 0.7636 (pt0) cc_final: 0.7383 (pm20) REVERT: C 109 GLU cc_start: 0.7637 (tp30) cc_final: 0.7239 (mm-30) REVERT: C 114 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7873 (t80) REVERT: C 124 GLN cc_start: 0.8423 (mt0) cc_final: 0.7805 (tm-30) REVERT: C 202 GLU cc_start: 0.4173 (OUTLIER) cc_final: 0.3600 (tp30) REVERT: C 216 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5371 (tp) REVERT: C 272 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: C 300 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7809 (mmm) REVERT: C 328 SER cc_start: 0.7954 (m) cc_final: 0.7666 (t) REVERT: C 330 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7260 (tt0) outliers start: 25 outliers final: 4 residues processed: 100 average time/residue: 1.4840 time to fit residues: 153.5406 Evaluate side-chains 96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 50.0000 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 4713 Z= 0.464 Angle : 0.682 6.937 6405 Z= 0.344 Chirality : 0.045 0.126 733 Planarity : 0.006 0.042 840 Dihedral : 6.711 54.167 641 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.26 % Allowed : 15.01 % Favored : 80.73 % 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: 0.54 (0.33), residues: 574 helix: 1.00 (0.36), residues: 218 sheet: 1.83 (0.55), residues: 78 loop : -0.57 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 81 HIS 0.007 0.001 HIS C 163 PHE 0.026 0.003 PHE C 314 TYR 0.014 0.003 TYR C 278 ARG 0.005 0.001 ARG E 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8982 (tt0) cc_final: 0.8690 (tt0) REVERT: E 69 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6008 (ptpt) REVERT: E 83 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7866 (mm-40) REVERT: E 112 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7340 (ttp-170) REVERT: E 116 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7889 (ptmt) REVERT: E 125 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7821 (mm-30) REVERT: E 198 GLN cc_start: 0.6893 (mt0) cc_final: 0.6442 (tp40) REVERT: E 348 GLN cc_start: 0.7578 (pt0) cc_final: 0.7219 (pt0) REVERT: C 109 GLU cc_start: 0.7757 (tp30) cc_final: 0.7351 (mm-30) REVERT: C 124 GLN cc_start: 0.8446 (mt0) cc_final: 0.7772 (tm-30) REVERT: C 202 GLU cc_start: 0.4390 (OUTLIER) cc_final: 0.3792 (tp30) REVERT: C 216 ILE cc_start: 0.5823 (OUTLIER) cc_final: 0.5373 (tp) REVERT: C 233 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7143 (mtt-85) REVERT: C 252 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7805 (mt-10) REVERT: C 272 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: C 300 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7857 (mmm) REVERT: C 330 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7224 (tt0) outliers start: 21 outliers final: 5 residues processed: 94 average time/residue: 1.4856 time to fit residues: 144.2035 Evaluate side-chains 94 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4713 Z= 0.273 Angle : 0.569 6.343 6405 Z= 0.288 Chirality : 0.040 0.119 733 Planarity : 0.005 0.036 840 Dihedral : 6.462 53.067 641 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.67 % Allowed : 15.62 % Favored : 79.72 % 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: 0.67 (0.34), residues: 574 helix: 1.15 (0.36), residues: 218 sheet: 1.77 (0.56), residues: 78 loop : -0.49 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.004 0.001 HIS C 163 PHE 0.022 0.002 PHE C 314 TYR 0.011 0.002 TYR C 278 ARG 0.007 0.001 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8964 (tt0) cc_final: 0.8694 (tt0) REVERT: E 69 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.5958 (ptpt) REVERT: E 83 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7726 (mm-40) REVERT: E 112 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.7342 (ttp-170) REVERT: E 124 GLN cc_start: 0.8400 (mt0) cc_final: 0.8130 (mt0) REVERT: E 125 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7824 (mm-30) REVERT: E 158 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8426 (mm) REVERT: E 198 GLN cc_start: 0.6843 (mt0) cc_final: 0.6535 (tp-100) REVERT: E 219 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.5731 (pmtt) REVERT: E 348 GLN cc_start: 0.7492 (pt0) cc_final: 0.7122 (pt0) REVERT: C 109 GLU cc_start: 0.7709 (tp30) cc_final: 0.7306 (mm-30) REVERT: C 114 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7818 (t80) REVERT: C 124 GLN cc_start: 0.8440 (mt0) cc_final: 0.7772 (tm-30) REVERT: C 216 ILE cc_start: 0.5763 (OUTLIER) cc_final: 0.5296 (tp) REVERT: C 233 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7197 (mtt-85) REVERT: C 252 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7812 (mt-10) REVERT: C 272 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: C 300 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: C 330 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7252 (tt0) outliers start: 23 outliers final: 5 residues processed: 99 average time/residue: 1.3783 time to fit residues: 141.1706 Evaluate side-chains 94 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 10 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: E 134 GLN C 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4713 Z= 0.139 Angle : 0.484 5.727 6405 Z= 0.243 Chirality : 0.037 0.118 733 Planarity : 0.004 0.034 840 Dihedral : 6.077 52.874 641 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.85 % Allowed : 16.63 % Favored : 79.51 % 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: 0.97 (0.34), residues: 574 helix: 1.42 (0.37), residues: 219 sheet: 1.61 (0.56), residues: 83 loop : -0.27 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 81 HIS 0.003 0.001 HIS C 101 PHE 0.018 0.002 PHE C 314 TYR 0.009 0.001 TYR E 278 ARG 0.006 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8922 (tt0) cc_final: 0.8680 (tt0) REVERT: E 69 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.5840 (ptpt) REVERT: E 83 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7503 (mm-40) REVERT: E 112 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7339 (ttp-170) REVERT: E 124 GLN cc_start: 0.8380 (mt0) cc_final: 0.8070 (mt0) REVERT: E 125 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7821 (mm-30) REVERT: E 219 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.5760 (pmtt) REVERT: E 348 GLN cc_start: 0.7317 (pt0) cc_final: 0.6965 (pt0) REVERT: C 83 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: C 109 GLU cc_start: 0.7638 (tp30) cc_final: 0.7173 (mm-30) REVERT: C 114 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7970 (t80) REVERT: C 124 GLN cc_start: 0.8425 (mt0) cc_final: 0.7812 (tm-30) REVERT: C 216 ILE cc_start: 0.5613 (OUTLIER) cc_final: 0.5172 (tp) REVERT: C 233 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7181 (mtt-85) REVERT: C 252 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7889 (mt-10) REVERT: C 272 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: C 300 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7800 (mmm) REVERT: C 328 SER cc_start: 0.7907 (m) cc_final: 0.7653 (t) outliers start: 19 outliers final: 6 residues processed: 98 average time/residue: 1.4393 time to fit residues: 145.8297 Evaluate side-chains 99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4713 Z= 0.318 Angle : 0.593 6.150 6405 Z= 0.297 Chirality : 0.042 0.136 733 Planarity : 0.005 0.035 840 Dihedral : 6.364 53.353 641 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.45 % Allowed : 17.85 % Favored : 78.70 % 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: 0.78 (0.34), residues: 574 helix: 1.27 (0.37), residues: 218 sheet: 1.66 (0.56), residues: 78 loop : -0.40 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 81 HIS 0.005 0.001 HIS C 163 PHE 0.022 0.003 PHE C 314 TYR 0.013 0.002 TYR E 278 ARG 0.006 0.001 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8969 (tt0) cc_final: 0.8688 (tt0) REVERT: E 69 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.5963 (ptpt) REVERT: E 83 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7695 (mm-40) REVERT: E 112 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7344 (ttp-170) REVERT: E 125 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7907 (mm-30) REVERT: E 198 GLN cc_start: 0.6792 (mt0) cc_final: 0.6369 (tp40) REVERT: E 219 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.5787 (pmtt) REVERT: E 348 GLN cc_start: 0.7496 (pt0) cc_final: 0.7117 (pt0) REVERT: C 109 GLU cc_start: 0.7744 (tp30) cc_final: 0.7273 (mm-30) REVERT: C 114 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7879 (t80) REVERT: C 124 GLN cc_start: 0.8445 (mt0) cc_final: 0.7783 (tm-30) REVERT: C 216 ILE cc_start: 0.5749 (OUTLIER) cc_final: 0.5286 (tp) REVERT: C 233 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7206 (mtt-85) REVERT: C 252 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7817 (mt-10) REVERT: C 272 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: C 300 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7828 (mmm) outliers start: 17 outliers final: 5 residues processed: 92 average time/residue: 1.5154 time to fit residues: 143.8043 Evaluate side-chains 98 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 56 optimal weight: 7.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4713 Z= 0.169 Angle : 0.505 5.729 6405 Z= 0.254 Chirality : 0.038 0.121 733 Planarity : 0.004 0.033 840 Dihedral : 6.136 52.486 641 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.45 % Allowed : 18.26 % Favored : 78.30 % 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: 0.98 (0.34), residues: 574 helix: 1.43 (0.37), residues: 218 sheet: 1.66 (0.57), residues: 78 loop : -0.23 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS C 101 PHE 0.019 0.002 PHE C 314 TYR 0.013 0.002 TYR E 278 ARG 0.007 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8935 (tt0) cc_final: 0.8676 (tt0) REVERT: E 69 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.5859 (ptpt) REVERT: E 83 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7535 (mm-40) REVERT: E 112 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7350 (ttp-170) REVERT: E 124 GLN cc_start: 0.8397 (mt0) cc_final: 0.8123 (mt0) REVERT: E 125 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7898 (mm-30) REVERT: E 219 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.5743 (pmtt) REVERT: E 348 GLN cc_start: 0.7387 (pt0) cc_final: 0.7017 (pt0) REVERT: C 83 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: C 109 GLU cc_start: 0.7678 (tp30) cc_final: 0.7202 (mm-30) REVERT: C 114 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7862 (t80) REVERT: C 124 GLN cc_start: 0.8434 (mt0) cc_final: 0.7797 (tm-30) REVERT: C 202 GLU cc_start: 0.4197 (OUTLIER) cc_final: 0.3633 (tp30) REVERT: C 216 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5161 (tp) REVERT: C 233 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7148 (mtt-85) REVERT: C 252 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7877 (mt-10) REVERT: C 300 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7811 (mmm) REVERT: C 328 SER cc_start: 0.7906 (m) cc_final: 0.7637 (t) outliers start: 17 outliers final: 5 residues processed: 97 average time/residue: 1.4071 time to fit residues: 141.1066 Evaluate side-chains 96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4713 Z= 0.253 Angle : 0.556 5.917 6405 Z= 0.278 Chirality : 0.040 0.119 733 Planarity : 0.004 0.034 840 Dihedral : 6.248 52.810 641 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.25 % Allowed : 18.26 % Favored : 78.50 % 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: 0.94 (0.34), residues: 574 helix: 1.37 (0.37), residues: 218 sheet: 1.65 (0.57), residues: 78 loop : -0.25 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 81 HIS 0.004 0.001 HIS C 163 PHE 0.021 0.002 PHE C 314 TYR 0.014 0.002 TYR E 278 ARG 0.008 0.000 ARG E 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8960 (tt0) cc_final: 0.8700 (tt0) REVERT: E 69 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.5937 (ptpt) REVERT: E 83 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7619 (mm-40) REVERT: E 112 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.7347 (ttp-170) REVERT: E 125 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 219 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.5761 (pmtt) REVERT: E 348 GLN cc_start: 0.7448 (pt0) cc_final: 0.7070 (pt0) REVERT: C 109 GLU cc_start: 0.7719 (tp30) cc_final: 0.7149 (mm-30) REVERT: C 114 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7869 (t80) REVERT: C 124 GLN cc_start: 0.8445 (mt0) cc_final: 0.7791 (tm-30) REVERT: C 202 GLU cc_start: 0.4256 (OUTLIER) cc_final: 0.3679 (tp30) REVERT: C 216 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.5239 (tp) REVERT: C 233 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7147 (mtt-85) REVERT: C 252 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7887 (mt-10) REVERT: C 300 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7823 (mmm) REVERT: C 330 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7280 (tt0) outliers start: 16 outliers final: 5 residues processed: 93 average time/residue: 1.5034 time to fit residues: 144.4002 Evaluate side-chains 96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.148260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.119171 restraints weight = 4920.114| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.83 r_work: 0.3064 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4713 Z= 0.175 Angle : 0.511 5.744 6405 Z= 0.256 Chirality : 0.038 0.124 733 Planarity : 0.004 0.033 840 Dihedral : 6.112 52.351 641 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.65 % Allowed : 18.26 % Favored : 78.09 % 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: 1.04 (0.34), residues: 574 helix: 1.43 (0.37), residues: 219 sheet: 1.65 (0.58), residues: 78 loop : -0.15 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS C 101 PHE 0.019 0.002 PHE C 314 TYR 0.016 0.002 TYR E 278 ARG 0.007 0.000 ARG E 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.23 seconds wall clock time: 54 minutes 32.34 seconds (3272.34 seconds total)