Starting phenix.real_space_refine on Mon Jan 13 19:37:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrj_39543/01_2025/8yrj_39543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrj_39543/01_2025/8yrj_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/cci-nas-00/data/ceres_data/8yrj_39543/01_2025/8yrj_39543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrj_39543/01_2025/8yrj_39543.map" model { file = "/net/cci-nas-00/data/ceres_data/8yrj_39543/01_2025/8yrj_39543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrj_39543/01_2025/8yrj_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 3.07, per 1000 atoms: 0.82 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 1.33 Conformation dependent library (CDL) restraints added in 429.7 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: 0.37 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: 0.98 Time building geometry restraints manager: 1.14 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: 0.00 - 1.24: 5021 1.24 - 2.47: 117 2.47 - 3.71: 24 3.71 - 4.95: 12 4.95 - 6.18: 9 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: 1.330 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.090 Find NCS groups from input model: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.382 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: 0.1655 time to fit residues: 38.2434 Evaluate side-chains 125 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.182055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.156994 restraints weight = 7675.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160946 restraints weight = 4726.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.163654 restraints weight = 3305.564| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 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 to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.390 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: 0.8170 (p90) cc_final: 0.7769 (p90) REVERT: A 137 TRP cc_start: 0.7137 (m-10) cc_final: 0.6620 (m-10) REVERT: A 144 TYR cc_start: 0.7100 (m-80) cc_final: 0.6761 (m-10) REVERT: A 222 LEU cc_start: 0.8701 (tt) cc_final: 0.8125 (tp) REVERT: H 33 PHE cc_start: 0.8825 (t80) cc_final: 0.8388 (t80) REVERT: H 37 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8582 (mm) REVERT: B 51 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8080 (mm-30) REVERT: B 79 ASP cc_start: 0.8414 (m-30) cc_final: 0.8167 (p0) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.1479 time to fit residues: 25.8994 Evaluate side-chains 130 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.176241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151089 restraints weight = 7550.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154980 restraints weight = 4582.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.157571 restraints weight = 3217.222| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3823 Z= 0.227 Angle : 0.784 12.610 5183 Z= 0.378 Chirality : 0.048 0.217 638 Planarity : 0.003 0.031 615 Dihedral : 10.350 58.378 677 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.93 % Favored : 94.62 % Rotamer: Outliers : 3.99 % Allowed : 21.95 % Favored : 74.06 % 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: 1.38 (0.40), residues: 446 helix: 2.23 (0.32), residues: 237 sheet: 0.56 (0.65), residues: 67 loop : -1.25 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 134 HIS 0.007 0.001 HIS A 65 PHE 0.011 0.002 PHE B 45 TYR 0.027 0.002 TYR H 26 ARG 0.004 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 146 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7703 (tt0) cc_final: 0.7028 (tm-30) REVERT: A 127 PHE cc_start: 0.8396 (p90) cc_final: 0.8031 (p90) REVERT: A 144 TYR cc_start: 0.7069 (m-80) cc_final: 0.6699 (m-10) REVERT: H 33 PHE cc_start: 0.8684 (t80) cc_final: 0.8474 (t80) REVERT: B 79 ASP cc_start: 0.8470 (m-30) cc_final: 0.8228 (p0) outliers start: 16 outliers final: 11 residues processed: 139 average time/residue: 0.1384 time to fit residues: 24.1944 Evaluate side-chains 132 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.178400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.152563 restraints weight = 7582.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.156279 restraints weight = 4605.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.158731 restraints weight = 3266.585| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3823 Z= 0.213 Angle : 0.730 9.379 5183 Z= 0.353 Chirality : 0.047 0.235 638 Planarity : 0.003 0.029 615 Dihedral : 8.005 57.977 677 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.93 % Favored : 94.39 % Rotamer: Outliers : 3.99 % Allowed : 24.94 % Favored : 71.07 % 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: 1.60 (0.41), residues: 446 helix: 2.66 (0.32), residues: 228 sheet: 0.04 (0.72), residues: 55 loop : -0.96 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 137 HIS 0.002 0.001 HIS A 132 PHE 0.025 0.002 PHE A 40 TYR 0.024 0.002 TYR H 26 ARG 0.003 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 to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8348 (p90) cc_final: 0.8006 (p90) REVERT: A 144 TYR cc_start: 0.7000 (m-80) cc_final: 0.6652 (m-10) REVERT: H 33 PHE cc_start: 0.8647 (t80) cc_final: 0.7575 (t80) REVERT: B 79 ASP cc_start: 0.8482 (m-30) cc_final: 0.8258 (p0) REVERT: B 103 SER cc_start: 0.7968 (m) cc_final: 0.7692 (m) outliers start: 16 outliers final: 14 residues processed: 143 average time/residue: 0.1328 time to fit residues: 23.8654 Evaluate side-chains 142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 205 LEU 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 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 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 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.0570 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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** B 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.174950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149995 restraints weight = 7618.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.153919 restraints weight = 4488.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.156447 restraints weight = 3063.127| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3823 Z= 0.204 Angle : 0.725 9.293 5183 Z= 0.359 Chirality : 0.046 0.227 638 Planarity : 0.003 0.036 615 Dihedral : 7.024 56.165 677 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.38 % Favored : 93.95 % Rotamer: Outliers : 4.74 % Allowed : 24.69 % Favored : 70.57 % 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: 1.59 (0.40), residues: 446 helix: 2.59 (0.32), residues: 224 sheet: 0.29 (0.71), residues: 55 loop : -0.87 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 137 HIS 0.002 0.001 HIS A 65 PHE 0.022 0.002 PHE H 33 TYR 0.020 0.001 TYR B 193 ARG 0.001 0.000 ARG A 162 *********************** 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 148 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.6993 (m-80) cc_final: 0.6521 (m-10) REVERT: A 218 ASP cc_start: 0.7247 (t0) cc_final: 0.6912 (t0) REVERT: B 148 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.5937 (t80) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 0.1379 time to fit residues: 24.2487 Evaluate side-chains 139 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE 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 197 LYS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 PHE 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 148 PHE Chi-restraints excluded: chain B residue 161 ASP 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 7 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.177831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151634 restraints weight = 7346.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.155538 restraints weight = 4346.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.158233 restraints weight = 3029.435| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3823 Z= 0.189 Angle : 0.745 10.017 5183 Z= 0.364 Chirality : 0.047 0.237 638 Planarity : 0.003 0.032 615 Dihedral : 6.621 56.142 677 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.93 % Favored : 94.39 % Rotamer: Outliers : 4.49 % Allowed : 26.18 % Favored : 69.33 % 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: 1.62 (0.40), residues: 446 helix: 2.62 (0.32), residues: 222 sheet: 0.54 (0.72), residues: 55 loop : -0.93 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.002 0.001 HIS A 65 PHE 0.023 0.002 PHE B 168 TYR 0.022 0.001 TYR B 193 ARG 0.002 0.000 ARG A 162 *********************** 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 147 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.6914 (m-80) cc_final: 0.6442 (m-10) REVERT: A 204 GLN cc_start: 0.8432 (tt0) cc_final: 0.8040 (tp40) REVERT: B 52 PHE cc_start: 0.8497 (t80) cc_final: 0.8234 (t80) REVERT: B 79 ASP cc_start: 0.8532 (p0) cc_final: 0.8239 (m-30) REVERT: B 103 SER cc_start: 0.8003 (m) cc_final: 0.7721 (m) REVERT: B 148 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6058 (t80) outliers start: 18 outliers final: 15 residues processed: 142 average time/residue: 0.1349 time to fit residues: 24.0338 Evaluate side-chains 142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 197 LYS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.175206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148731 restraints weight = 7437.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.152546 restraints weight = 4414.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.155200 restraints weight = 3090.341| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3823 Z= 0.220 Angle : 0.739 11.859 5183 Z= 0.362 Chirality : 0.046 0.236 638 Planarity : 0.003 0.032 615 Dihedral : 6.510 55.097 677 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.71 % Favored : 94.62 % Rotamer: Outliers : 4.74 % Allowed : 26.43 % Favored : 68.83 % 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: 1.54 (0.41), residues: 446 helix: 2.54 (0.32), residues: 222 sheet: 0.58 (0.73), residues: 55 loop : -0.97 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 95 HIS 0.003 0.001 HIS A 132 PHE 0.016 0.002 PHE B 168 TYR 0.017 0.002 TYR B 193 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 150 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7520 (tp-100) cc_final: 0.7093 (tp-100) REVERT: A 144 TYR cc_start: 0.7000 (m-80) cc_final: 0.6453 (m-10) REVERT: A 204 GLN cc_start: 0.8441 (tt0) cc_final: 0.8096 (tp40) REVERT: A 218 ASP cc_start: 0.7129 (t0) cc_final: 0.6857 (t0) REVERT: H 52 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8561 (mmmt) REVERT: B 51 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7866 (mt-10) REVERT: B 103 SER cc_start: 0.8130 (m) cc_final: 0.7845 (m) outliers start: 19 outliers final: 17 residues processed: 142 average time/residue: 0.1311 time to fit residues: 23.6000 Evaluate side-chains 145 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 198 CYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 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 139 MET 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 28 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.175189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.149357 restraints weight = 7296.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.153277 restraints weight = 4283.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.155978 restraints weight = 2965.951| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3823 Z= 0.211 Angle : 0.764 12.154 5183 Z= 0.374 Chirality : 0.048 0.279 638 Planarity : 0.003 0.032 615 Dihedral : 6.509 55.345 677 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.48 % Favored : 94.84 % Rotamer: Outliers : 4.99 % Allowed : 27.18 % Favored : 67.83 % 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: 1.43 (0.40), residues: 446 helix: 2.43 (0.32), residues: 222 sheet: 0.58 (0.72), residues: 55 loop : -1.00 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 95 HIS 0.002 0.001 HIS A 65 PHE 0.014 0.002 PHE A 127 TYR 0.025 0.001 TYR B 92 ARG 0.001 0.000 ARG B 194 *********************** 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 153 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7494 (tp-100) cc_final: 0.7074 (tp-100) REVERT: A 144 TYR cc_start: 0.6939 (m-80) cc_final: 0.6440 (m-10) REVERT: A 174 CYS cc_start: 0.2843 (p) cc_final: 0.1349 (p) REVERT: A 202 TRP cc_start: 0.8999 (p-90) cc_final: 0.8507 (p-90) REVERT: A 204 GLN cc_start: 0.8435 (tt0) cc_final: 0.8087 (tp40) REVERT: A 218 ASP cc_start: 0.7292 (t0) cc_final: 0.7091 (t0) REVERT: H 52 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8552 (mmmt) REVERT: B 51 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7899 (mt-10) REVERT: B 148 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6009 (t80) outliers start: 20 outliers final: 13 residues processed: 146 average time/residue: 0.1257 time to fit residues: 23.1702 Evaluate side-chains 145 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 198 CYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G 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 148 PHE 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 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.173612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147268 restraints weight = 7425.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150939 restraints weight = 4471.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153367 restraints weight = 3176.109| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3823 Z= 0.216 Angle : 0.779 13.063 5183 Z= 0.378 Chirality : 0.047 0.312 638 Planarity : 0.003 0.032 615 Dihedral : 6.576 54.927 677 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.71 % Favored : 94.62 % 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: 1.40 (0.40), residues: 446 helix: 2.44 (0.32), residues: 223 sheet: 0.47 (0.75), residues: 53 loop : -1.04 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 63 HIS 0.003 0.001 HIS A 132 PHE 0.014 0.002 PHE A 207 TYR 0.020 0.002 TYR B 92 ARG 0.001 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 154 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.7430 (pm20) cc_final: 0.7213 (pm20) REVERT: A 202 TRP cc_start: 0.8960 (p-90) cc_final: 0.8500 (p-90) REVERT: A 204 GLN cc_start: 0.8345 (tt0) cc_final: 0.8077 (tp40) REVERT: H 52 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8480 (mmmt) REVERT: B 51 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7878 (mt-10) REVERT: B 103 SER cc_start: 0.8215 (m) cc_final: 0.7910 (m) REVERT: B 148 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6067 (t80) outliers start: 19 outliers final: 15 residues processed: 145 average time/residue: 0.1343 time to fit residues: 24.4666 Evaluate side-chains 147 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 198 CYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 34 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 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 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.168241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140500 restraints weight = 7744.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.144557 restraints weight = 4529.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.147393 restraints weight = 3143.693| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3823 Z= 0.260 Angle : 0.821 14.443 5183 Z= 0.401 Chirality : 0.049 0.387 638 Planarity : 0.003 0.035 615 Dihedral : 6.683 54.299 677 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.16 % Favored : 94.17 % Rotamer: Outliers : 3.99 % Allowed : 30.67 % 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: 1.16 (0.40), residues: 446 helix: 2.24 (0.31), residues: 223 sheet: 0.39 (0.73), residues: 54 loop : -1.18 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 95 HIS 0.003 0.001 HIS A 173 PHE 0.027 0.002 PHE B 52 TYR 0.020 0.002 TYR B 92 ARG 0.008 0.001 ARG H 45 ********************** 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 150 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.8119 (m-10) cc_final: 0.7769 (m-10) REVERT: A 144 TYR cc_start: 0.6852 (m-10) cc_final: 0.6313 (m-10) REVERT: A 184 GLU cc_start: 0.7475 (pm20) cc_final: 0.7259 (pm20) REVERT: A 202 TRP cc_start: 0.9079 (p-90) cc_final: 0.8561 (p-90) REVERT: A 204 GLN cc_start: 0.8536 (tt0) cc_final: 0.8175 (tp40) REVERT: H 43 TYR cc_start: 0.8516 (m-10) cc_final: 0.8295 (m-10) REVERT: B 103 SER cc_start: 0.8425 (m) cc_final: 0.8198 (m) REVERT: B 148 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.5949 (t80) outliers start: 16 outliers final: 14 residues processed: 142 average time/residue: 0.1298 time to fit residues: 23.3265 Evaluate side-chains 146 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 198 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 31 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** B 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.170991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.143162 restraints weight = 7545.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.147252 restraints weight = 4411.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.150180 restraints weight = 3061.931| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3823 Z= 0.232 Angle : 0.827 13.278 5183 Z= 0.408 Chirality : 0.049 0.355 638 Planarity : 0.003 0.033 615 Dihedral : 6.753 54.704 677 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.16 % Favored : 94.17 % Rotamer: Outliers : 3.74 % Allowed : 30.92 % 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: 1.23 (0.40), residues: 446 helix: 2.24 (0.31), residues: 226 sheet: 0.60 (0.74), residues: 55 loop : -1.20 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 95 HIS 0.004 0.001 HIS A 173 PHE 0.023 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: 1502.53 seconds wall clock time: 27 minutes 43.66 seconds (1663.66 seconds total)