Starting phenix.real_space_refine on Fri Aug 2 16:57:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrj_39543/08_2024/8yrj_39543.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrj_39543/08_2024/8yrj_39543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrj_39543/08_2024/8yrj_39543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrj_39543/08_2024/8yrj_39543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrj_39543/08_2024/8yrj_39543.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yrj_39543/08_2024/8yrj_39543.cif" } resolution = 3.87 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= -0.000 sd= 0.006 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 21 5.16 5 C 2442 2.51 5 N 597 2.21 5 O 688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3748 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1743 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 208} Chain: "G" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "H" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 341 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.91, per 1000 atoms: 0.78 Number of scatterers: 3748 At special positions: 0 Unit cell: (57.27, 74.7, 118.69, 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 21 16.00 O 688 8.00 N 597 7.00 C 2442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS H 25 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 163 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 301 " - " ASN A 73 " " NAG A 302 " - " ASN A 167 " " NAG A 303 " - " ASN A 152 " " NAG C 1 " - " ASN A 66 " " NAG D 1 " - " ASN A 106 " Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 632.5 milliseconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 6 sheets defined 56.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 236 Processing helix chain 'G' and resid 23 through 58 Processing helix chain 'H' and resid 21 through 62 removed outlier: 3.945A pdb=" N CYS H 25 " --> pdb=" O GLU H 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 75 removed outlier: 5.267A pdb=" N LYS B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 117 through 154 removed outlier: 4.115A pdb=" N GLY B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 199 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.638A pdb=" N THR A 108 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 removed outlier: 4.289A pdb=" N TYR A 177 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS A 141 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 142 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR A 153 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR A 144 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.766A pdb=" N GLY A 125 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE A 127 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ARG A 162 " --> pdb=" O PHE A 127 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 732 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: 1.03 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1124 1.35 - 1.46: 980 1.46 - 1.58: 1692 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 3823 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 3818 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 83 107.46 - 114.10: 2285 114.10 - 120.73: 1569 120.73 - 127.36: 1216 127.36 - 133.99: 30 Bond angle restraints: 5183 Sorted by residual: angle pdb=" C CYS A 198 " pdb=" N LYS A 199 " pdb=" CA LYS A 199 " ideal model delta sigma weight residual 121.54 126.03 -4.49 1.91e+00 2.74e-01 5.53e+00 angle pdb=" C GLN B 40 " pdb=" N THR B 41 " pdb=" CA THR B 41 " ideal model delta sigma weight residual 121.54 125.78 -4.24 1.91e+00 2.74e-01 4.93e+00 angle pdb=" N GLU H 21 " pdb=" CA GLU H 21 " pdb=" C GLU H 21 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.50e+00 angle pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" O2 BMA C 3 " ideal model delta sigma weight residual 112.95 106.77 6.18 3.00e+00 1.11e-01 4.25e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.79 6.16 3.00e+00 1.11e-01 4.22e+00 ... (remaining 5178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 2161 23.39 - 46.78: 161 46.78 - 70.17: 25 70.17 - 93.56: 17 93.56 - 116.95: 11 Dihedral angle restraints: 2375 sinusoidal: 1042 harmonic: 1333 Sorted by residual: dihedral pdb=" CB CYS G 25 " pdb=" SG CYS G 25 " pdb=" SG CYS H 25 " pdb=" CB CYS H 25 " ideal model delta sinusoidal sigma weight residual 93.00 174.20 -81.20 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" C1 NAG C 2 " pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C4 NAG C 2 " ideal model delta sinusoidal sigma weight residual -64.11 52.84 -116.95 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C1 NAG C 2 " pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C6 NAG C 2 " ideal model delta sinusoidal sigma weight residual 171.16 -72.39 -116.45 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 2372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 540 0.054 - 0.108: 82 0.108 - 0.161: 14 0.161 - 0.215: 0 0.215 - 0.269: 2 Chirality restraints: 638 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2 BMA C 3 " pdb=" C1 BMA C 3 " pdb=" C3 BMA C 3 " pdb=" O2 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 635 not shown) Planarity restraints: 620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 207 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 208 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 157 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO A 158 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 56 " -0.005 2.00e-02 2.50e+03 9.38e-03 8.79e-01 pdb=" C GLN A 56 " 0.016 2.00e-02 2.50e+03 pdb=" O GLN A 56 " -0.006 2.00e-02 2.50e+03 pdb=" N MET A 57 " -0.005 2.00e-02 2.50e+03 ... (remaining 617 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 654 2.77 - 3.30: 3630 3.30 - 3.84: 6313 3.84 - 4.37: 6566 4.37 - 4.90: 11859 Nonbonded interactions: 29022 Sorted by model distance: nonbonded pdb=" O ASP A 168 " pdb=" OH TYR A 172 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" N TRP B 42 " model vdw 2.352 3.120 nonbonded pdb=" OG SER A 154 " pdb=" O SER A 157 " model vdw 2.356 3.040 nonbonded pdb=" O LEU A 221 " pdb=" OG1 THR A 225 " model vdw 2.364 3.040 nonbonded pdb=" O ASP A 86 " pdb=" OH TYR A 90 " model vdw 2.375 3.040 ... (remaining 29017 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' selection = chain 'D' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 22 through 58) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.060 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 0.083 3823 Z= 0.194 Angle : 0.542 6.185 5183 Z= 0.256 Chirality : 0.042 0.269 638 Planarity : 0.003 0.033 615 Dihedral : 19.292 116.955 1505 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.59 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.39 (0.42), residues: 446 helix: 3.31 (0.31), residues: 232 sheet: 0.83 (0.61), residues: 71 loop : -1.08 (0.58), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 42 HIS 0.001 0.000 HIS A 173 PHE 0.006 0.001 PHE B 168 TYR 0.007 0.001 TYR A 50 ARG 0.001 0.000 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8195 (tttt) cc_final: 0.7872 (ttpt) REVERT: A 93 GLN cc_start: 0.7156 (tt0) cc_final: 0.6787 (tm-30) REVERT: A 128 ASP cc_start: 0.8230 (m-30) cc_final: 0.7993 (m-30) REVERT: A 144 TYR cc_start: 0.7097 (m-80) cc_final: 0.6446 (m-80) REVERT: A 203 LEU cc_start: 0.9533 (mt) cc_final: 0.9281 (mt) REVERT: H 33 PHE cc_start: 0.8736 (t80) cc_final: 0.8306 (t80) REVERT: B 109 ILE cc_start: 0.9025 (mm) cc_final: 0.8642 (mm) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1633 time to fit residues: 37.4846 Evaluate side-chains 125 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3823 Z= 0.240 Angle : 0.778 11.567 5183 Z= 0.377 Chirality : 0.050 0.298 638 Planarity : 0.004 0.035 615 Dihedral : 14.815 84.794 677 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.48 % Favored : 94.84 % Rotamer: Outliers : 4.49 % Allowed : 20.95 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.83 (0.40), residues: 446 helix: 3.00 (0.31), residues: 226 sheet: -0.08 (0.63), residues: 68 loop : -1.03 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 137 HIS 0.008 0.002 HIS A 173 PHE 0.030 0.002 PHE B 45 TYR 0.043 0.002 TYR H 26 ARG 0.004 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8230 (p90) cc_final: 0.7825 (p90) REVERT: A 130 ARG cc_start: 0.7712 (ttp80) cc_final: 0.7477 (ptt90) REVERT: A 137 TRP cc_start: 0.7173 (m-10) cc_final: 0.6633 (m-10) REVERT: A 144 TYR cc_start: 0.7176 (m-80) cc_final: 0.6808 (m-10) REVERT: A 222 LEU cc_start: 0.8728 (tt) cc_final: 0.8188 (tp) REVERT: H 33 PHE cc_start: 0.8857 (t80) cc_final: 0.8448 (t80) REVERT: H 37 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8580 (mm) REVERT: B 51 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8090 (mm-30) REVERT: B 79 ASP cc_start: 0.8404 (m-30) cc_final: 0.8151 (p0) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.1404 time to fit residues: 24.5913 Evaluate side-chains 131 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3823 Z= 0.288 Angle : 0.817 12.506 5183 Z= 0.394 Chirality : 0.049 0.231 638 Planarity : 0.004 0.032 615 Dihedral : 10.978 64.138 677 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.48 % Favored : 95.07 % Rotamer: Outliers : 4.49 % Allowed : 21.95 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.25 (0.40), residues: 446 helix: 2.17 (0.32), residues: 236 sheet: 0.44 (0.63), residues: 68 loop : -1.35 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 95 HIS 0.010 0.002 HIS A 65 PHE 0.014 0.002 PHE B 52 TYR 0.028 0.002 TYR H 26 ARG 0.005 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.8147 (m-80) cc_final: 0.7918 (m-10) REVERT: A 93 GLN cc_start: 0.8009 (tt0) cc_final: 0.7170 (tm-30) REVERT: A 127 PHE cc_start: 0.8490 (p90) cc_final: 0.8139 (p90) REVERT: A 130 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7641 (ptt90) REVERT: A 144 TYR cc_start: 0.7260 (m-80) cc_final: 0.6794 (m-10) REVERT: A 204 GLN cc_start: 0.8744 (tp40) cc_final: 0.8244 (tp40) REVERT: B 79 ASP cc_start: 0.8467 (m-30) cc_final: 0.8263 (p0) outliers start: 18 outliers final: 14 residues processed: 145 average time/residue: 0.1364 time to fit residues: 24.5804 Evaluate side-chains 138 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3823 Z= 0.229 Angle : 0.743 9.728 5183 Z= 0.358 Chirality : 0.048 0.251 638 Planarity : 0.003 0.029 615 Dihedral : 8.007 59.941 677 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.71 % Favored : 94.62 % Rotamer: Outliers : 3.99 % Allowed : 26.93 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.59 (0.41), residues: 446 helix: 2.55 (0.32), residues: 227 sheet: -0.05 (0.64), residues: 63 loop : -0.74 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 137 HIS 0.003 0.001 HIS A 65 PHE 0.027 0.002 PHE A 40 TYR 0.021 0.002 TYR A 200 ARG 0.002 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.8171 (m-80) cc_final: 0.7862 (m-10) REVERT: A 127 PHE cc_start: 0.8497 (p90) cc_final: 0.8141 (p90) REVERT: A 130 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7795 (ptt90) REVERT: A 135 LYS cc_start: 0.8344 (ttpt) cc_final: 0.8118 (tptp) REVERT: A 144 TYR cc_start: 0.7184 (m-80) cc_final: 0.6760 (m-10) REVERT: A 204 GLN cc_start: 0.8737 (tp40) cc_final: 0.8181 (tp40) REVERT: B 155 LYS cc_start: 0.7394 (mmtp) cc_final: 0.6847 (pttp) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.1162 time to fit residues: 20.8785 Evaluate side-chains 140 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3823 Z= 0.311 Angle : 0.789 9.254 5183 Z= 0.391 Chirality : 0.050 0.238 638 Planarity : 0.004 0.040 615 Dihedral : 7.394 57.809 677 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.48 % Favored : 94.84 % Rotamer: Outliers : 7.48 % Allowed : 22.94 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.90 (0.39), residues: 446 helix: 2.09 (0.32), residues: 222 sheet: -0.04 (0.67), residues: 56 loop : -1.27 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 95 HIS 0.004 0.001 HIS A 65 PHE 0.017 0.002 PHE B 52 TYR 0.016 0.002 TYR B 92 ARG 0.002 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.8311 (m-80) cc_final: 0.7693 (m-10) REVERT: A 130 ARG cc_start: 0.8255 (ttp80) cc_final: 0.8053 (ptt90) REVERT: A 135 LYS cc_start: 0.8322 (ttpt) cc_final: 0.8117 (tptp) REVERT: A 144 TYR cc_start: 0.7352 (m-80) cc_final: 0.6801 (m-10) REVERT: B 79 ASP cc_start: 0.8513 (m-30) cc_final: 0.8284 (p0) REVERT: B 103 SER cc_start: 0.8312 (m) cc_final: 0.8074 (m) REVERT: B 148 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6135 (t80) outliers start: 30 outliers final: 19 residues processed: 154 average time/residue: 0.1340 time to fit residues: 25.7851 Evaluate side-chains 150 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3823 Z= 0.235 Angle : 0.770 9.818 5183 Z= 0.378 Chirality : 0.049 0.307 638 Planarity : 0.003 0.033 615 Dihedral : 7.062 58.571 677 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.48 % Favored : 94.84 % Rotamer: Outliers : 4.74 % Allowed : 27.93 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.08 (0.40), residues: 446 helix: 2.24 (0.32), residues: 225 sheet: -0.26 (0.64), residues: 63 loop : -1.17 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 95 HIS 0.002 0.001 HIS A 65 PHE 0.028 0.003 PHE A 127 TYR 0.020 0.002 TYR H 26 ARG 0.002 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.8317 (m-80) cc_final: 0.7720 (m-10) REVERT: A 93 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 129 ILE cc_start: 0.8941 (mp) cc_final: 0.8595 (mp) REVERT: A 130 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7831 (ptt90) REVERT: A 144 TYR cc_start: 0.7269 (m-80) cc_final: 0.6675 (m-10) REVERT: B 103 SER cc_start: 0.8249 (m) cc_final: 0.7979 (m) REVERT: B 148 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.5962 (t80) REVERT: B 150 TYR cc_start: 0.9016 (t80) cc_final: 0.8714 (t80) REVERT: B 155 LYS cc_start: 0.7534 (mmtp) cc_final: 0.6824 (pttp) outliers start: 19 outliers final: 16 residues processed: 149 average time/residue: 0.1358 time to fit residues: 25.2034 Evaluate side-chains 153 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3823 Z= 0.233 Angle : 0.774 9.905 5183 Z= 0.384 Chirality : 0.049 0.333 638 Planarity : 0.003 0.032 615 Dihedral : 6.865 56.735 677 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.48 % Favored : 94.84 % Rotamer: Outliers : 5.49 % Allowed : 28.93 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.05 (0.40), residues: 446 helix: 2.28 (0.32), residues: 225 sheet: -0.52 (0.62), residues: 63 loop : -1.16 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 137 HIS 0.002 0.001 HIS A 65 PHE 0.037 0.003 PHE A 127 TYR 0.022 0.002 TYR B 92 ARG 0.002 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.8346 (m-80) cc_final: 0.7769 (m-10) REVERT: A 93 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 148 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.5942 (t80) REVERT: B 150 TYR cc_start: 0.9028 (t80) cc_final: 0.8728 (t80) outliers start: 22 outliers final: 19 residues processed: 149 average time/residue: 0.1336 time to fit residues: 24.9103 Evaluate side-chains 154 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3823 Z= 0.250 Angle : 0.803 10.541 5183 Z= 0.400 Chirality : 0.049 0.327 638 Planarity : 0.003 0.030 615 Dihedral : 6.876 55.554 677 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.48 % Favored : 94.84 % Rotamer: Outliers : 5.99 % Allowed : 28.68 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.87 (0.40), residues: 446 helix: 2.01 (0.32), residues: 225 sheet: -0.38 (0.62), residues: 63 loop : -1.14 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 137 HIS 0.002 0.001 HIS A 65 PHE 0.036 0.002 PHE A 127 TYR 0.020 0.002 TYR A 201 ARG 0.003 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6247 (tpt) cc_final: 0.5912 (tmm) REVERT: A 90 TYR cc_start: 0.8363 (m-80) cc_final: 0.7805 (m-10) REVERT: A 130 ARG cc_start: 0.7764 (ptm-80) cc_final: 0.7388 (ptt90) REVERT: B 148 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.5908 (t80) REVERT: B 150 TYR cc_start: 0.9040 (t80) cc_final: 0.8622 (t80) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.1391 time to fit residues: 26.1233 Evaluate side-chains 152 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3823 Z= 0.255 Angle : 0.851 12.429 5183 Z= 0.418 Chirality : 0.049 0.317 638 Planarity : 0.003 0.032 615 Dihedral : 6.838 54.864 677 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.26 % Favored : 95.07 % Rotamer: Outliers : 4.74 % Allowed : 30.67 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.89 (0.40), residues: 446 helix: 2.03 (0.31), residues: 225 sheet: -0.11 (0.63), residues: 63 loop : -1.26 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 137 HIS 0.003 0.001 HIS A 173 PHE 0.034 0.002 PHE A 127 TYR 0.020 0.002 TYR B 92 ARG 0.002 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.7661 (m) cc_final: 0.6976 (t) REVERT: A 57 MET cc_start: 0.6209 (tpt) cc_final: 0.5800 (tmm) REVERT: A 90 TYR cc_start: 0.8368 (m-80) cc_final: 0.7810 (m-10) REVERT: A 93 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 236 GLN cc_start: 0.7386 (tm-30) cc_final: 0.6049 (tt0) REVERT: B 148 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.5889 (t80) outliers start: 19 outliers final: 17 residues processed: 152 average time/residue: 0.1433 time to fit residues: 26.8573 Evaluate side-chains 152 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 3823 Z= 0.274 Angle : 0.832 11.469 5183 Z= 0.413 Chirality : 0.050 0.319 638 Planarity : 0.003 0.031 615 Dihedral : 6.830 54.023 677 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.05 % Favored : 93.27 % Rotamer: Outliers : 4.49 % Allowed : 31.17 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.80 (0.39), residues: 446 helix: 1.93 (0.31), residues: 226 sheet: -0.24 (0.63), residues: 63 loop : -1.25 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 202 HIS 0.003 0.001 HIS A 173 PHE 0.032 0.002 PHE A 127 TYR 0.021 0.002 TYR A 201 ARG 0.002 0.000 ARG B 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6245 (tpt) cc_final: 0.5899 (tmm) REVERT: A 90 TYR cc_start: 0.8391 (m-80) cc_final: 0.7909 (m-10) REVERT: A 130 ARG cc_start: 0.7790 (ptm-80) cc_final: 0.7430 (ptt90) REVERT: A 135 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8054 (tmmt) REVERT: A 184 GLU cc_start: 0.7478 (pm20) cc_final: 0.6668 (pt0) REVERT: A 236 GLN cc_start: 0.7329 (tm-30) cc_final: 0.5994 (tt0) REVERT: B 103 SER cc_start: 0.8332 (m) cc_final: 0.8090 (m) REVERT: B 148 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.5979 (t80) REVERT: B 159 GLU cc_start: 0.7718 (pt0) cc_final: 0.7444 (pt0) outliers start: 18 outliers final: 14 residues processed: 148 average time/residue: 0.1376 time to fit residues: 25.4633 Evaluate side-chains 145 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.0070 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.0170 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.172236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146171 restraints weight = 7464.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.149777 restraints weight = 4594.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.152421 restraints weight = 3262.997| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.7174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 3823 Z= 0.243 Angle : 0.809 10.485 5183 Z= 0.398 Chirality : 0.047 0.329 638 Planarity : 0.003 0.030 615 Dihedral : 6.694 54.142 677 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.90 % Allowed : 4.26 % Favored : 94.84 % Rotamer: Outliers : 2.99 % Allowed : 32.67 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.83 (0.39), residues: 446 helix: 1.95 (0.31), residues: 226 sheet: -0.21 (0.63), residues: 63 loop : -1.24 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 95 HIS 0.002 0.001 HIS A 173 PHE 0.031 0.002 PHE A 127 TYR 0.018 0.002 TYR B 92 ARG 0.002 0.000 ARG B 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1200.01 seconds wall clock time: 21 minutes 52.61 seconds (1312.61 seconds total)