Starting phenix.real_space_refine on Tue Feb 13 08:39:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csy_26975/02_2024/8csy_26975.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csy_26975/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csy_26975/02_2024/8csy_26975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csy_26975/02_2024/8csy_26975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csy_26975/02_2024/8csy_26975.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csy_26975/02_2024/8csy_26975.pdb" } 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 Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.03, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 1.99 Conformation dependent library (CDL) restraints added in 865.9 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: 0.52 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: 1.15 Time building geometry restraints manager: 2.15 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: 99.53 - 106.43: 174 106.43 - 113.34: 2600 113.34 - 120.24: 1601 120.24 - 127.14: 1965 127.14 - 134.04: 65 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 2.440 nonbonded pdb=" NH2 ARG E 292 " pdb=" O LYS E 353 " model vdw 2.304 2.520 nonbonded pdb=" OD1 ASP E 316 " pdb=" NE1 TRP C 105 " model vdw 2.305 2.520 nonbonded pdb=" O ALA E 331 " pdb=" OG SER E 334 " model vdw 2.310 2.440 nonbonded pdb=" OD2 ASP C 122 " pdb=" O HOH C1001 " model vdw 2.328 2.440 ... (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 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: 0.800 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: 3.920 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.290 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.180 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.575 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: 1.4209 time to fit residues: 180.2352 Evaluate side-chains 103 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.8449 moved from start: 0.1174 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= 0.257 Angle : 0.554 6.062 6405 Z= 0.279 Chirality : 0.040 0.137 733 Planarity : 0.005 0.036 840 Dihedral : 7.065 59.599 647 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.67 % Allowed : 12.98 % Favored : 82.35 % 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: 1.13 (0.34), residues: 574 helix: 1.35 (0.36), residues: 219 sheet: 2.28 (0.56), residues: 78 loop : -0.15 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 81 HIS 0.003 0.001 HIS E 309 PHE 0.021 0.002 PHE C 314 TYR 0.010 0.002 TYR E 278 ARG 0.003 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 116 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: E 69 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5748 (ptpt) REVERT: E 112 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7355 (ttp-170) REVERT: E 125 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7845 (mm-30) REVERT: E 198 GLN cc_start: 0.6744 (mt0) cc_final: 0.6360 (tp40) REVERT: E 219 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.5785 (pmtt) REVERT: E 233 ARG cc_start: 0.8393 (mtm180) cc_final: 0.8182 (mtm180) REVERT: E 239 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: E 348 GLN cc_start: 0.7461 (pt0) cc_final: 0.7178 (pt0) REVERT: C 83 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: C 109 GLU cc_start: 0.7622 (tp30) cc_final: 0.7153 (mm-30) REVERT: C 114 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7820 (t80) REVERT: C 124 GLN cc_start: 0.8420 (mt0) cc_final: 0.7783 (tm-30) REVERT: C 155 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7636 (ttp-110) REVERT: C 198 GLN cc_start: 0.7824 (tt0) cc_final: 0.7327 (mt0) REVERT: C 202 GLU cc_start: 0.4170 (OUTLIER) cc_final: 0.3581 (tp30) REVERT: C 272 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: C 300 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7827 (mmm) REVERT: C 330 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7218 (tt0) outliers start: 23 outliers final: 5 residues processed: 104 average time/residue: 1.4160 time to fit residues: 151.9632 Evaluate side-chains 102 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 239 GLN 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: 4.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.8465 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4713 Z= 0.297 Angle : 0.576 6.401 6405 Z= 0.289 Chirality : 0.041 0.126 733 Planarity : 0.005 0.036 840 Dihedral : 6.577 52.142 644 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.67 % Allowed : 14.40 % Favored : 80.93 % 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: 1.29 (0.36), residues: 218 sheet: 2.09 (0.55), residues: 78 loop : -0.32 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 E 278 ARG 0.004 0.001 ARG E 304 *********************** 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 111 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: E 69 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.5856 (ptpt) REVERT: E 83 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7806 (mm-40) REVERT: E 112 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7352 (ttp-170) REVERT: E 116 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7957 (ptmt) REVERT: E 125 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7932 (mm-30) REVERT: E 198 GLN cc_start: 0.6796 (mt0) cc_final: 0.6392 (tp40) REVERT: E 219 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.5778 (pmtt) REVERT: E 233 ARG cc_start: 0.8404 (mtm180) cc_final: 0.8182 (mtm180) REVERT: E 239 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: E 348 GLN cc_start: 0.7512 (pt0) cc_final: 0.7174 (pt0) REVERT: C 83 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: C 109 GLU cc_start: 0.7651 (tp30) cc_final: 0.7239 (mm-30) REVERT: C 114 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7825 (t80) REVERT: C 124 GLN cc_start: 0.8420 (mt0) cc_final: 0.7769 (tm-30) REVERT: C 155 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7663 (ttp-110) REVERT: C 198 GLN cc_start: 0.7812 (tt0) cc_final: 0.7205 (mt0) REVERT: C 202 GLU cc_start: 0.4222 (OUTLIER) cc_final: 0.3647 (tp30) REVERT: C 216 ILE cc_start: 0.5830 (OUTLIER) cc_final: 0.5402 (tp) REVERT: C 272 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: C 300 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7828 (mmm) REVERT: C 330 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7251 (tt0) outliers start: 23 outliers final: 6 residues processed: 101 average time/residue: 1.4346 time to fit residues: 149.4500 Evaluate side-chains 103 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 239 GLN Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 91 ASN 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 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: 1.9990 chunk 34 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8445 moved from start: 0.1439 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= 0.211 Angle : 0.514 5.865 6405 Z= 0.258 Chirality : 0.039 0.129 733 Planarity : 0.004 0.035 840 Dihedral : 6.373 51.942 644 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.27 % Allowed : 13.39 % Favored : 81.34 % 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: 1.06 (0.34), residues: 574 helix: 1.42 (0.36), residues: 218 sheet: 2.10 (0.56), residues: 78 loop : -0.26 (0.35), 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 163 PHE 0.021 0.002 PHE C 314 TYR 0.011 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 112 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8927 (tt0) cc_final: 0.8672 (tt0) REVERT: E 69 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.5813 (ptpt) REVERT: E 83 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7723 (mm-40) REVERT: E 112 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7363 (ttp-170) REVERT: E 116 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7906 (ptmt) REVERT: E 125 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7923 (mm-30) REVERT: E 158 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8403 (mm) REVERT: E 198 GLN cc_start: 0.6747 (mt0) cc_final: 0.6389 (tp40) REVERT: E 219 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.5663 (pmtt) REVERT: E 233 ARG cc_start: 0.8379 (mtm180) cc_final: 0.8158 (mtm180) REVERT: E 348 GLN cc_start: 0.7454 (pt0) cc_final: 0.7138 (pt0) REVERT: C 83 GLN cc_start: 0.7687 (pt0) cc_final: 0.7396 (pm20) REVERT: C 109 GLU cc_start: 0.7652 (tp30) cc_final: 0.7227 (mm-30) REVERT: C 114 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7888 (t80) REVERT: C 124 GLN cc_start: 0.8413 (mt0) cc_final: 0.7778 (tm-30) REVERT: C 155 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7638 (ttp-110) REVERT: C 198 GLN cc_start: 0.7790 (tt0) cc_final: 0.7120 (mm110) REVERT: C 202 GLU cc_start: 0.4235 (OUTLIER) cc_final: 0.3654 (tp30) REVERT: C 216 ILE cc_start: 0.5795 (OUTLIER) cc_final: 0.5345 (tp) REVERT: C 272 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: C 300 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7824 (mmm) REVERT: C 330 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7237 (tt0) outliers start: 26 outliers final: 6 residues processed: 101 average time/residue: 1.4353 time to fit residues: 149.6963 Evaluate side-chains 102 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 155 ARG 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 325 ASP Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 332 LEU 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: 7.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 40.0000 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4713 Z= 0.411 Angle : 0.643 6.715 6405 Z= 0.322 Chirality : 0.044 0.124 733 Planarity : 0.005 0.036 840 Dihedral : 6.610 53.749 641 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 0.66 (0.33), residues: 574 helix: 1.13 (0.36), residues: 218 sheet: 1.91 (0.55), residues: 78 loop : -0.53 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 81 HIS 0.007 0.001 HIS C 163 PHE 0.025 0.003 PHE C 314 TYR 0.012 0.003 TYR E 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 107 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8966 (tt0) cc_final: 0.8675 (tt0) REVERT: E 69 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.5958 (ptpt) REVERT: E 83 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7822 (mm-40) REVERT: E 112 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7348 (ttp-170) REVERT: E 116 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7960 (ptmt) REVERT: E 125 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7834 (mm-30) REVERT: E 198 GLN cc_start: 0.6874 (mt0) cc_final: 0.6426 (tp40) REVERT: E 219 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.5795 (pmtt) REVERT: E 233 ARG cc_start: 0.8393 (mtm180) cc_final: 0.8180 (mtm180) REVERT: E 348 GLN cc_start: 0.7575 (pt0) cc_final: 0.7212 (pt0) REVERT: C 109 GLU cc_start: 0.7754 (tp30) cc_final: 0.7349 (mm-30) REVERT: C 124 GLN cc_start: 0.8425 (mt0) cc_final: 0.7755 (tm-30) REVERT: C 155 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7685 (ttp-110) REVERT: C 198 GLN cc_start: 0.7811 (tt0) cc_final: 0.7161 (mm110) REVERT: C 202 GLU cc_start: 0.4364 (OUTLIER) cc_final: 0.3780 (tp30) REVERT: C 216 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5397 (tp) REVERT: C 252 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7828 (mt-10) REVERT: C 272 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: C 300 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7850 (mmm) REVERT: C 330 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7252 (tt0) outliers start: 23 outliers final: 6 residues processed: 98 average time/residue: 1.3874 time to fit residues: 140.4425 Evaluate side-chains 99 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 166 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.8463 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4713 Z= 0.257 Angle : 0.550 6.193 6405 Z= 0.277 Chirality : 0.039 0.121 733 Planarity : 0.004 0.036 840 Dihedral : 6.384 52.674 641 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.26 % Allowed : 16.23 % 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: 0.77 (0.34), residues: 574 helix: 1.25 (0.36), residues: 218 sheet: 1.89 (0.55), residues: 78 loop : -0.47 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.005 0.001 HIS C 163 PHE 0.022 0.002 PHE C 314 TYR 0.011 0.002 TYR E 278 ARG 0.004 0.000 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 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8942 (tt0) cc_final: 0.8657 (tt0) REVERT: E 69 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.5880 (ptpt) REVERT: E 83 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7712 (mm-40) REVERT: E 112 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7362 (ttp-170) REVERT: E 116 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7987 (ptmt) REVERT: E 124 GLN cc_start: 0.8374 (mt0) cc_final: 0.8114 (mt0) REVERT: E 125 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7831 (mm-30) REVERT: E 158 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8431 (mm) REVERT: E 198 GLN cc_start: 0.6808 (mt0) cc_final: 0.6368 (tp40) REVERT: E 219 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.5797 (pmtt) REVERT: E 233 ARG cc_start: 0.8352 (mtm180) cc_final: 0.8139 (mtm180) REVERT: E 348 GLN cc_start: 0.7508 (pt0) cc_final: 0.7136 (pt0) REVERT: C 83 GLN cc_start: 0.7727 (pt0) cc_final: 0.7434 (pm20) REVERT: C 109 GLU cc_start: 0.7722 (tp30) cc_final: 0.7308 (mm-30) REVERT: C 114 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7827 (t80) REVERT: C 124 GLN cc_start: 0.8422 (mt0) cc_final: 0.7759 (tm-30) REVERT: C 155 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7659 (ttp-110) REVERT: C 198 GLN cc_start: 0.7798 (tt0) cc_final: 0.7143 (mm110) REVERT: C 202 GLU cc_start: 0.4324 (OUTLIER) cc_final: 0.3751 (tp30) REVERT: C 216 ILE cc_start: 0.5781 (OUTLIER) cc_final: 0.5322 (tp) REVERT: C 272 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: C 300 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: C 330 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7240 (tt0) outliers start: 21 outliers final: 5 residues processed: 98 average time/residue: 1.3893 time to fit residues: 140.7725 Evaluate side-chains 101 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 91 ASN 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 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 Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.8438 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4713 Z= 0.176 Angle : 0.497 5.704 6405 Z= 0.249 Chirality : 0.038 0.124 733 Planarity : 0.004 0.034 840 Dihedral : 6.150 51.857 641 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.46 % Allowed : 16.43 % Favored : 79.11 % 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: 1.01 (0.34), residues: 574 helix: 1.41 (0.36), residues: 219 sheet: 2.01 (0.56), residues: 78 loop : -0.31 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 81 HIS 0.003 0.001 HIS C 163 PHE 0.020 0.002 PHE C 314 TYR 0.010 0.001 TYR E 278 ARG 0.005 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 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8914 (tt0) cc_final: 0.8632 (tt0) REVERT: E 69 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.5849 (ptpt) REVERT: E 83 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7634 (mm-40) REVERT: E 112 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7369 (ttp-170) REVERT: E 124 GLN cc_start: 0.8355 (mt0) cc_final: 0.8105 (mt0) REVERT: E 125 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7900 (mm-30) REVERT: E 126 THR cc_start: 0.8263 (t) cc_final: 0.7922 (m) REVERT: E 158 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8376 (mm) REVERT: E 219 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.5779 (pmtt) REVERT: E 233 ARG cc_start: 0.8329 (mtm180) cc_final: 0.8116 (mtm180) REVERT: E 291 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: E 348 GLN cc_start: 0.7439 (pt0) cc_final: 0.7078 (pt0) REVERT: C 83 GLN cc_start: 0.7684 (pt0) cc_final: 0.7419 (pm20) REVERT: C 109 GLU cc_start: 0.7684 (tp30) cc_final: 0.7200 (mm-30) REVERT: C 114 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7887 (t80) REVERT: C 124 GLN cc_start: 0.8420 (mt0) cc_final: 0.7772 (tm-30) REVERT: C 155 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7624 (ttp-110) REVERT: C 198 GLN cc_start: 0.7787 (tt0) cc_final: 0.7126 (mm110) REVERT: C 202 GLU cc_start: 0.4267 (OUTLIER) cc_final: 0.3706 (tp30) REVERT: C 216 ILE cc_start: 0.5718 (OUTLIER) cc_final: 0.5259 (tp) REVERT: C 272 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: C 300 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7829 (mmm) REVERT: C 330 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7253 (tt0) outliers start: 22 outliers final: 6 residues processed: 97 average time/residue: 1.4366 time to fit residues: 143.9986 Evaluate side-chains 100 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 E residue 291 GLU Chi-restraints excluded: chain C residue 91 ASN 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 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 325 ASP Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8453 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4713 Z= 0.231 Angle : 0.530 5.928 6405 Z= 0.265 Chirality : 0.039 0.120 733 Planarity : 0.004 0.034 840 Dihedral : 6.211 52.657 641 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.26 % Allowed : 16.84 % Favored : 78.90 % 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: 1.39 (0.37), residues: 219 sheet: 1.93 (0.56), residues: 78 loop : -0.31 (0.35), residues: 277 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 0.010 0.002 TYR E 278 ARG 0.003 0.000 ARG C 292 *********************** 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 106 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8933 (tt0) cc_final: 0.8656 (tt0) REVERT: E 69 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.5925 (ptpt) REVERT: E 83 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7682 (mm-40) REVERT: E 112 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7360 (ttp-170) REVERT: E 125 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7917 (mm-30) REVERT: E 198 GLN cc_start: 0.6732 (mt0) cc_final: 0.6355 (tp40) REVERT: E 219 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.5768 (pmtt) REVERT: E 233 ARG cc_start: 0.8344 (mtm180) cc_final: 0.8134 (mtm180) REVERT: E 348 GLN cc_start: 0.7494 (pt0) cc_final: 0.7110 (pt0) REVERT: C 83 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7424 (pm20) REVERT: C 109 GLU cc_start: 0.7751 (tp30) cc_final: 0.7174 (mm-30) REVERT: C 114 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7877 (t80) REVERT: C 124 GLN cc_start: 0.8421 (mt0) cc_final: 0.7773 (tm-30) REVERT: C 155 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7634 (ttp-110) REVERT: C 198 GLN cc_start: 0.7785 (tt0) cc_final: 0.7125 (mm110) REVERT: C 202 GLU cc_start: 0.4296 (OUTLIER) cc_final: 0.3732 (tp30) REVERT: C 216 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.5290 (tp) REVERT: C 272 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: C 300 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: C 330 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7237 (tt0) outliers start: 21 outliers final: 8 residues processed: 98 average time/residue: 1.3780 time to fit residues: 139.8805 Evaluate side-chains 103 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 49 THR Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 91 ASN 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 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 325 ASP Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4713 Z= 0.163 Angle : 0.489 5.453 6405 Z= 0.243 Chirality : 0.037 0.123 733 Planarity : 0.004 0.033 840 Dihedral : 6.026 51.711 641 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.85 % Allowed : 17.85 % 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: 1.14 (0.35), residues: 574 helix: 1.53 (0.37), residues: 219 sheet: 1.83 (0.55), residues: 83 loop : -0.19 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 81 HIS 0.003 0.001 HIS C 101 PHE 0.019 0.002 PHE C 314 TYR 0.009 0.001 TYR E 278 ARG 0.006 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 108 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8907 (tt0) cc_final: 0.8631 (tt0) REVERT: E 69 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.5881 (ptpt) REVERT: E 83 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7597 (mm-40) REVERT: E 112 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7344 (ttp-170) REVERT: E 124 GLN cc_start: 0.8338 (mt0) cc_final: 0.8051 (mt0) REVERT: E 125 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7808 (mm-30) REVERT: E 126 THR cc_start: 0.8250 (t) cc_final: 0.7921 (m) REVERT: E 158 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8376 (mm) REVERT: E 219 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.5748 (pmtt) REVERT: E 233 ARG cc_start: 0.8319 (mtm180) cc_final: 0.8106 (mtm180) REVERT: E 348 GLN cc_start: 0.7424 (pt0) cc_final: 0.7034 (pt0) REVERT: C 83 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: C 109 GLU cc_start: 0.7745 (tp30) cc_final: 0.7181 (mm-30) REVERT: C 114 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7868 (t80) REVERT: C 124 GLN cc_start: 0.8412 (mt0) cc_final: 0.7785 (tm-30) REVERT: C 155 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7605 (ttp-110) REVERT: C 198 GLN cc_start: 0.7768 (tt0) cc_final: 0.7122 (mm110) REVERT: C 202 GLU cc_start: 0.4218 (OUTLIER) cc_final: 0.3682 (tp30) REVERT: C 216 ILE cc_start: 0.5663 (OUTLIER) cc_final: 0.5211 (tp) REVERT: C 272 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: C 300 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7825 (mmm) outliers start: 19 outliers final: 6 residues processed: 100 average time/residue: 1.3519 time to fit residues: 139.9265 Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 83 GLN Chi-restraints excluded: chain C residue 91 ASN 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 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 325 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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: 0.1701 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= 0.265 Angle : 0.562 6.040 6405 Z= 0.279 Chirality : 0.040 0.142 733 Planarity : 0.004 0.034 840 Dihedral : 6.235 53.264 641 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.85 % Allowed : 18.05 % 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: 1.01 (0.34), residues: 574 helix: 1.39 (0.37), residues: 219 sheet: 1.92 (0.56), residues: 78 loop : -0.25 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 81 HIS 0.004 0.001 HIS C 163 PHE 0.021 0.002 PHE C 314 TYR 0.012 0.002 TYR E 278 ARG 0.005 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 106 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8941 (tt0) cc_final: 0.8661 (tt0) REVERT: E 69 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.5966 (ptpt) REVERT: E 83 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7692 (mm-40) REVERT: E 112 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7353 (ttp-170) REVERT: E 124 GLN cc_start: 0.8353 (mt0) cc_final: 0.8087 (mt0) REVERT: E 125 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7901 (mm-30) REVERT: E 198 GLN cc_start: 0.6736 (mt0) cc_final: 0.6364 (tp40) REVERT: E 219 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.5771 (pmtt) REVERT: E 233 ARG cc_start: 0.8351 (mtm180) cc_final: 0.8143 (mtm180) REVERT: E 348 GLN cc_start: 0.7507 (pt0) cc_final: 0.7114 (pt0) REVERT: C 83 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: C 109 GLU cc_start: 0.7791 (tp30) cc_final: 0.7151 (mm-30) REVERT: C 114 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7880 (t80) REVERT: C 124 GLN cc_start: 0.8418 (mt0) cc_final: 0.7774 (tm-30) REVERT: C 155 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7665 (ttp-110) REVERT: C 198 GLN cc_start: 0.7788 (tt0) cc_final: 0.7129 (mm110) REVERT: C 202 GLU cc_start: 0.4303 (OUTLIER) cc_final: 0.3741 (tp30) REVERT: C 216 ILE cc_start: 0.5757 (OUTLIER) cc_final: 0.5282 (tp) REVERT: C 272 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: C 300 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7832 (mmm) REVERT: C 330 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7237 (tt0) outliers start: 19 outliers final: 8 residues processed: 98 average time/residue: 1.4415 time to fit residues: 145.8302 Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 49 THR Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 91 ASN 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 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 325 ASP 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: 7.9990 chunk 18 optimal weight: 0.0970 chunk 46 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.150274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121519 restraints weight = 4945.386| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.82 r_work: 0.3093 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4713 Z= 0.124 Angle : 0.476 6.358 6405 Z= 0.235 Chirality : 0.037 0.126 733 Planarity : 0.004 0.032 840 Dihedral : 5.866 51.792 641 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.04 % Allowed : 19.27 % Favored : 77.69 % 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: 1.38 (0.35), residues: 574 helix: 1.67 (0.37), residues: 219 sheet: 1.80 (0.52), residues: 95 loop : -0.02 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 81 HIS 0.002 0.001 HIS C 101 PHE 0.017 0.001 PHE C 314 TYR 0.012 0.001 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: 3058.67 seconds wall clock time: 54 minutes 29.54 seconds (3269.54 seconds total)