Starting phenix.real_space_refine on Sat May 10 17:18:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8il3_35526/05_2025/8il3_35526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8il3_35526/05_2025/8il3_35526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8il3_35526/05_2025/8il3_35526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8il3_35526/05_2025/8il3_35526.map" model { file = "/net/cci-nas-00/data/ceres_data/8il3_35526/05_2025/8il3_35526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8il3_35526/05_2025/8il3_35526.cif" } resolution = 3.86 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1762 atoms to isotropic. 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 24 5.16 5 C 3255 2.51 5 N 888 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5172 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1682 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1609 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "C" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1881 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Time building chain proxies: 4.02, per 1000 atoms: 0.78 Number of scatterers: 5172 At special positions: 0 Unit cell: (68, 73.95, 128.35, 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 24 16.00 O 1005 8.00 N 888 7.00 C 3255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 59 " distance=2.97 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 640.2 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 17.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.134A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.518A pdb=" N GLY B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.679A pdb=" N PHE C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.957A pdb=" N ILE C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 233 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 5.905A pdb=" N LEU A 11 " --> pdb=" O GLU A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.611A pdb=" N PHE A 75 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.619A pdb=" N ALA A 134 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 185 " --> pdb=" O ALA A 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 152 through 154 removed outlier: 3.543A pdb=" N LYS A 211 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 166 through 167 Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AB4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.672A pdb=" N LEU B 143 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 185 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.672A pdb=" N LEU B 143 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 185 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AB8, first strand: chain 'C' and resid 179 through 181 removed outlier: 8.203A pdb=" N ASP C 179 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU C 215 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 181 " --> pdb=" O LEU C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.862A pdb=" N VAL C 219 " --> pdb=" O ILE C 255 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 357 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: 1.28 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1301 1.33 - 1.45: 1179 1.45 - 1.58: 2788 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5297 Sorted by residual: bond pdb=" N VAL B 189 " pdb=" CA VAL B 189 " ideal model delta sigma weight residual 1.461 1.493 -0.033 8.70e-03 1.32e+04 1.40e+01 bond pdb=" N ILE C 105 " pdb=" CA ILE C 105 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.22e-02 6.72e+03 1.08e+01 bond pdb=" N CYS C 157 " pdb=" CA CYS C 157 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N CYS C 231 " pdb=" CA CYS C 231 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 1.453 1.495 -0.042 1.31e-02 5.83e+03 1.01e+01 ... (remaining 5292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 6474 2.15 - 4.30: 604 4.30 - 6.45: 100 6.45 - 8.60: 16 8.60 - 10.75: 6 Bond angle restraints: 7200 Sorted by residual: angle pdb=" N PRO A 145 " pdb=" CA PRO A 145 " pdb=" C PRO A 145 " ideal model delta sigma weight residual 112.26 101.75 10.51 1.44e+00 4.82e-01 5.33e+01 angle pdb=" N VAL C 45 " pdb=" CA VAL C 45 " pdb=" C VAL C 45 " ideal model delta sigma weight residual 110.72 104.26 6.46 1.01e+00 9.80e-01 4.09e+01 angle pdb=" N PHE A 143 " pdb=" CA PHE A 143 " pdb=" C PHE A 143 " ideal model delta sigma weight residual 113.97 120.31 -6.34 1.28e+00 6.10e-01 2.45e+01 angle pdb=" N ASP C 229 " pdb=" CA ASP C 229 " pdb=" C ASP C 229 " ideal model delta sigma weight residual 111.56 104.50 7.06 1.43e+00 4.89e-01 2.44e+01 angle pdb=" N GLN C 84 " pdb=" CA GLN C 84 " pdb=" C GLN C 84 " ideal model delta sigma weight residual 109.81 120.33 -10.52 2.21e+00 2.05e-01 2.27e+01 ... (remaining 7195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2701 17.97 - 35.95: 336 35.95 - 53.92: 96 53.92 - 71.89: 27 71.89 - 89.87: 8 Dihedral angle restraints: 3168 sinusoidal: 1236 harmonic: 1932 Sorted by residual: dihedral pdb=" CB CYS C 44 " pdb=" SG CYS C 44 " pdb=" SG CYS C 59 " pdb=" CB CYS C 59 " ideal model delta sinusoidal sigma weight residual 93.00 -179.04 -87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA THR B 101 " pdb=" C THR B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA MET C 54 " pdb=" C MET C 54 " pdb=" N ARG C 55 " pdb=" CA ARG C 55 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 505 0.061 - 0.121: 177 0.121 - 0.182: 78 0.182 - 0.242: 31 0.242 - 0.303: 9 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA GLN C 84 " pdb=" N GLN C 84 " pdb=" C GLN C 84 " pdb=" CB GLN C 84 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA CYS C 44 " pdb=" N CYS C 44 " pdb=" C CYS C 44 " pdb=" CB CYS C 44 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL C 202 " pdb=" CA VAL C 202 " pdb=" CG1 VAL C 202 " pdb=" CG2 VAL C 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 797 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 105 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 106 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 106 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 106 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 101 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO B 102 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 199 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C PHE C 199 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE C 199 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY C 200 " 0.018 2.00e-02 2.50e+03 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1859 2.87 - 3.38: 4397 3.38 - 3.88: 8911 3.88 - 4.39: 9170 4.39 - 4.90: 15848 Nonbonded interactions: 40185 Sorted by model distance: nonbonded pdb=" O GLU C 238 " pdb=" OG SER C 241 " model vdw 2.362 3.040 nonbonded pdb=" O ARG C 35 " pdb=" OG1 THR C 39 " model vdw 2.366 3.040 nonbonded pdb=" O THR A 87 " pdb=" OG1 THR A 87 " model vdw 2.370 3.040 nonbonded pdb=" O GLU A 127 " pdb=" OG SER A 131 " model vdw 2.374 3.040 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 233 " model vdw 2.388 3.040 ... (remaining 40180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.950 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 16.130 Find NCS groups from input model: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.016 0.936 5298 Z= 0.846 Angle : 1.433 23.461 7202 Z= 0.893 Chirality : 0.084 0.303 800 Planarity : 0.010 0.080 928 Dihedral : 18.377 89.866 1919 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 8.75 % Allowed : 16.47 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.25), residues: 659 helix: -3.96 (0.24), residues: 116 sheet: -3.82 (0.32), residues: 167 loop : -3.10 (0.25), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 108 HIS 0.011 0.002 HIS B 35 PHE 0.038 0.004 PHE C 112 TYR 0.020 0.003 TYR B 107 ARG 0.008 0.001 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.26248 ( 127) hydrogen bonds : angle 9.80119 ( 357) SS BOND : bond 0.93563 ( 1) SS BOND : angle 21.92595 ( 2) covalent geometry : bond 0.00932 ( 5297) covalent geometry : angle 1.38594 ( 7200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 55 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8660 (mt) cc_final: 0.8376 (mp) REVERT: A 112 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.4337 (ppt170) REVERT: A 174 ASP cc_start: 0.6356 (p0) cc_final: 0.5614 (p0) REVERT: B 31 ASP cc_start: 0.8401 (t0) cc_final: 0.8018 (t70) REVERT: B 187 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7254 (m) REVERT: B 197 GLN cc_start: 0.2839 (OUTLIER) cc_final: 0.2553 (tm-30) outliers start: 51 outliers final: 17 residues processed: 102 average time/residue: 0.2097 time to fit residues: 26.5044 Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN C 25 GLN C 92 GLN C 116 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.100152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.085593 restraints weight = 18437.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087484 restraints weight = 12255.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.088823 restraints weight = 9120.376| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5298 Z= 0.147 Angle : 0.685 7.554 7202 Z= 0.356 Chirality : 0.043 0.129 800 Planarity : 0.006 0.060 928 Dihedral : 9.064 82.513 743 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.69 % Allowed : 18.01 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.28), residues: 659 helix: -2.06 (0.39), residues: 119 sheet: -3.33 (0.32), residues: 180 loop : -2.63 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 136 HIS 0.002 0.001 HIS B 59 PHE 0.011 0.001 PHE C 66 TYR 0.026 0.002 TYR A 144 ARG 0.004 0.001 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 127) hydrogen bonds : angle 6.69002 ( 357) SS BOND : bond 0.00734 ( 1) SS BOND : angle 2.29513 ( 2) covalent geometry : bond 0.00342 ( 5297) covalent geometry : angle 0.68378 ( 7200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 36 time to evaluate : 0.604 Fit side-chains REVERT: A 11 LEU cc_start: 0.8576 (mt) cc_final: 0.8357 (mp) REVERT: A 112 ARG cc_start: 0.5855 (OUTLIER) cc_final: 0.4333 (ppt170) REVERT: A 174 ASP cc_start: 0.6295 (p0) cc_final: 0.5715 (p0) REVERT: A 179 LEU cc_start: 0.9283 (tp) cc_final: 0.8433 (mp) REVERT: B 31 ASP cc_start: 0.8090 (t0) cc_final: 0.7737 (t70) REVERT: B 180 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8005 (mp) REVERT: C 25 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5741 (tm-30) REVERT: C 97 ASN cc_start: 0.7662 (m-40) cc_final: 0.7219 (m-40) outliers start: 39 outliers final: 22 residues processed: 73 average time/residue: 0.1556 time to fit residues: 15.3049 Evaluate side-chains 55 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 30 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN C 25 GLN C 51 HIS C 56 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.096698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.082459 restraints weight = 18955.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.084189 restraints weight = 12781.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.085488 restraints weight = 9621.874| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5298 Z= 0.182 Angle : 0.677 6.912 7202 Z= 0.351 Chirality : 0.043 0.125 800 Planarity : 0.005 0.054 928 Dihedral : 7.382 53.795 727 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 6.52 % Allowed : 20.75 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.29), residues: 659 helix: -1.44 (0.43), residues: 119 sheet: -3.19 (0.33), residues: 181 loop : -2.37 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.004 0.001 HIS B 59 PHE 0.017 0.002 PHE C 66 TYR 0.023 0.002 TYR A 144 ARG 0.004 0.001 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 127) hydrogen bonds : angle 6.44974 ( 357) SS BOND : bond 0.00559 ( 1) SS BOND : angle 1.53825 ( 2) covalent geometry : bond 0.00421 ( 5297) covalent geometry : angle 0.67675 ( 7200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 33 time to evaluate : 0.728 Fit side-chains REVERT: A 11 LEU cc_start: 0.8609 (mt) cc_final: 0.8351 (mp) REVERT: A 112 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.4476 (ppt170) REVERT: A 174 ASP cc_start: 0.6247 (p0) cc_final: 0.5704 (p0) REVERT: B 31 ASP cc_start: 0.8065 (t0) cc_final: 0.7746 (t70) REVERT: B 165 THR cc_start: 0.6061 (OUTLIER) cc_final: 0.5662 (m) REVERT: C 25 GLN cc_start: 0.6158 (OUTLIER) cc_final: 0.5914 (tm-30) outliers start: 38 outliers final: 26 residues processed: 68 average time/residue: 0.1745 time to fit residues: 15.7740 Evaluate side-chains 57 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 28 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 0.0370 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.098731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.084022 restraints weight = 18855.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.085859 restraints weight = 12434.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.087293 restraints weight = 9301.545| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5298 Z= 0.111 Angle : 0.596 6.491 7202 Z= 0.306 Chirality : 0.041 0.124 800 Planarity : 0.005 0.047 928 Dihedral : 6.440 55.306 725 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.60 % Allowed : 23.67 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.30), residues: 659 helix: -0.86 (0.45), residues: 119 sheet: -2.99 (0.33), residues: 181 loop : -2.24 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 108 HIS 0.002 0.001 HIS C 74 PHE 0.010 0.001 PHE A 75 TYR 0.016 0.001 TYR A 144 ARG 0.002 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 127) hydrogen bonds : angle 6.09011 ( 357) SS BOND : bond 0.00302 ( 1) SS BOND : angle 1.03167 ( 2) covalent geometry : bond 0.00256 ( 5297) covalent geometry : angle 0.59582 ( 7200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.604 Fit side-chains REVERT: A 11 LEU cc_start: 0.8590 (mt) cc_final: 0.8321 (mp) REVERT: A 112 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.4549 (ppt170) REVERT: A 174 ASP cc_start: 0.6329 (p0) cc_final: 0.5814 (p0) REVERT: B 31 ASP cc_start: 0.8102 (t0) cc_final: 0.7737 (t70) outliers start: 21 outliers final: 16 residues processed: 49 average time/residue: 0.2070 time to fit residues: 13.1329 Evaluate side-chains 45 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 28 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.097445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.082764 restraints weight = 18667.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.084621 restraints weight = 12497.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085954 restraints weight = 9339.134| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5298 Z= 0.126 Angle : 0.594 6.604 7202 Z= 0.303 Chirality : 0.042 0.123 800 Planarity : 0.004 0.045 928 Dihedral : 6.076 55.199 722 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.66 % Allowed : 21.44 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.30), residues: 659 helix: -0.60 (0.46), residues: 117 sheet: -2.78 (0.34), residues: 181 loop : -2.09 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 27 HIS 0.003 0.001 HIS C 56 PHE 0.012 0.001 PHE C 66 TYR 0.015 0.001 TYR A 53 ARG 0.003 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 127) hydrogen bonds : angle 5.96735 ( 357) SS BOND : bond 0.00510 ( 1) SS BOND : angle 1.08830 ( 2) covalent geometry : bond 0.00296 ( 5297) covalent geometry : angle 0.59361 ( 7200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 30 time to evaluate : 0.563 Fit side-chains REVERT: A 11 LEU cc_start: 0.8611 (mt) cc_final: 0.8317 (mp) REVERT: A 112 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.4538 (ppt170) REVERT: A 174 ASP cc_start: 0.6366 (p0) cc_final: 0.5848 (p0) REVERT: B 31 ASP cc_start: 0.8070 (t0) cc_final: 0.7729 (t70) outliers start: 33 outliers final: 26 residues processed: 60 average time/residue: 0.1641 time to fit residues: 13.2761 Evaluate side-chains 54 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 27 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 146 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.095113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.080635 restraints weight = 18971.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.082482 restraints weight = 12752.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.083779 restraints weight = 9498.856| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5298 Z= 0.205 Angle : 0.674 7.402 7202 Z= 0.344 Chirality : 0.044 0.139 800 Planarity : 0.005 0.047 928 Dihedral : 6.367 50.700 722 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.83 % Allowed : 22.47 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.31), residues: 659 helix: -0.92 (0.45), residues: 119 sheet: -2.95 (0.34), residues: 176 loop : -1.83 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 39 HIS 0.007 0.001 HIS C 51 PHE 0.019 0.002 PHE C 66 TYR 0.018 0.002 TYR A 144 ARG 0.004 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 127) hydrogen bonds : angle 6.24242 ( 357) SS BOND : bond 0.00630 ( 1) SS BOND : angle 1.52414 ( 2) covalent geometry : bond 0.00475 ( 5297) covalent geometry : angle 0.67318 ( 7200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 30 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8664 (mt) cc_final: 0.8331 (mp) REVERT: A 112 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.4562 (ppt170) REVERT: A 174 ASP cc_start: 0.6190 (p0) cc_final: 0.5710 (p0) REVERT: B 31 ASP cc_start: 0.8044 (t0) cc_final: 0.7713 (t70) REVERT: B 110 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7975 (pt0) outliers start: 34 outliers final: 25 residues processed: 61 average time/residue: 0.1645 time to fit residues: 13.4222 Evaluate side-chains 52 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 25 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 60 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.097115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.082759 restraints weight = 18413.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.084584 restraints weight = 12231.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.085894 restraints weight = 9119.910| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5298 Z= 0.116 Angle : 0.596 7.420 7202 Z= 0.300 Chirality : 0.042 0.124 800 Planarity : 0.004 0.045 928 Dihedral : 5.791 51.930 720 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.83 % Allowed : 22.98 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.31), residues: 659 helix: -0.48 (0.46), residues: 117 sheet: -2.78 (0.36), residues: 167 loop : -1.76 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 27 HIS 0.004 0.001 HIS C 51 PHE 0.012 0.001 PHE A 75 TYR 0.017 0.001 TYR A 53 ARG 0.002 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 127) hydrogen bonds : angle 5.90953 ( 357) SS BOND : bond 0.00395 ( 1) SS BOND : angle 0.86699 ( 2) covalent geometry : bond 0.00270 ( 5297) covalent geometry : angle 0.59556 ( 7200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 30 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8619 (mt) cc_final: 0.8319 (mp) REVERT: A 112 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.4496 (ppt170) REVERT: A 174 ASP cc_start: 0.6184 (p0) cc_final: 0.5776 (p0) REVERT: B 31 ASP cc_start: 0.8020 (t0) cc_final: 0.7694 (t70) REVERT: B 110 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7943 (pt0) outliers start: 34 outliers final: 30 residues processed: 61 average time/residue: 0.1685 time to fit residues: 14.0007 Evaluate side-chains 57 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 25 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 146 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.092982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.078926 restraints weight = 19309.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.080658 restraints weight = 13053.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.081898 restraints weight = 9796.057| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5298 Z= 0.241 Angle : 0.724 7.166 7202 Z= 0.372 Chirality : 0.044 0.154 800 Planarity : 0.005 0.052 928 Dihedral : 6.556 45.762 720 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 6.17 % Allowed : 22.98 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.31), residues: 659 helix: -1.06 (0.43), residues: 118 sheet: -2.84 (0.35), residues: 179 loop : -1.77 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 39 HIS 0.004 0.001 HIS C 182 PHE 0.023 0.002 PHE B 95 TYR 0.024 0.002 TYR A 144 ARG 0.003 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 127) hydrogen bonds : angle 6.52943 ( 357) SS BOND : bond 0.00773 ( 1) SS BOND : angle 1.97671 ( 2) covalent geometry : bond 0.00557 ( 5297) covalent geometry : angle 0.72301 ( 7200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 29 time to evaluate : 0.613 Fit side-chains REVERT: A 11 LEU cc_start: 0.8749 (mt) cc_final: 0.8350 (mp) REVERT: A 112 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.4778 (ppt170) REVERT: A 174 ASP cc_start: 0.6330 (p0) cc_final: 0.5790 (p0) REVERT: B 31 ASP cc_start: 0.8004 (t0) cc_final: 0.7642 (t70) REVERT: B 110 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7991 (pt0) REVERT: C 100 LEU cc_start: 0.7899 (tt) cc_final: 0.7621 (tt) outliers start: 36 outliers final: 31 residues processed: 60 average time/residue: 0.1621 time to fit residues: 13.4855 Evaluate side-chains 61 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 28 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 0.0030 chunk 40 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 HIS ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.096731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.082406 restraints weight = 18884.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.084254 restraints weight = 12557.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.085585 restraints weight = 9341.583| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5298 Z= 0.104 Angle : 0.595 8.163 7202 Z= 0.298 Chirality : 0.041 0.127 800 Planarity : 0.004 0.045 928 Dihedral : 5.759 50.473 720 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.63 % Allowed : 24.53 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.32), residues: 659 helix: -0.28 (0.47), residues: 117 sheet: -2.58 (0.37), residues: 167 loop : -1.69 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 27 HIS 0.003 0.001 HIS A 202 PHE 0.012 0.001 PHE A 75 TYR 0.008 0.001 TYR B 107 ARG 0.002 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 127) hydrogen bonds : angle 5.82492 ( 357) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.45546 ( 2) covalent geometry : bond 0.00237 ( 5297) covalent geometry : angle 0.59484 ( 7200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 31 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8627 (mt) cc_final: 0.8321 (mp) REVERT: A 112 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.4474 (ppt170) REVERT: A 174 ASP cc_start: 0.6167 (p0) cc_final: 0.5772 (p0) REVERT: B 31 ASP cc_start: 0.7935 (t0) cc_final: 0.7637 (t70) REVERT: B 110 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: C 100 LEU cc_start: 0.7525 (tt) cc_final: 0.7175 (tt) outliers start: 27 outliers final: 23 residues processed: 56 average time/residue: 0.1596 time to fit residues: 12.2383 Evaluate side-chains 53 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 28 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 18 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 48 optimal weight: 0.0170 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.097843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.083639 restraints weight = 18885.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.085482 restraints weight = 12505.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.086813 restraints weight = 9303.153| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5298 Z= 0.098 Angle : 0.574 8.602 7202 Z= 0.287 Chirality : 0.041 0.125 800 Planarity : 0.004 0.045 928 Dihedral : 5.420 53.366 720 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.77 % Allowed : 25.73 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.32), residues: 659 helix: 0.09 (0.49), residues: 117 sheet: -2.35 (0.38), residues: 163 loop : -1.63 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 102 HIS 0.005 0.001 HIS C 51 PHE 0.013 0.001 PHE A 75 TYR 0.018 0.001 TYR A 53 ARG 0.003 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 127) hydrogen bonds : angle 5.60109 ( 357) SS BOND : bond 0.00244 ( 1) SS BOND : angle 0.52151 ( 2) covalent geometry : bond 0.00228 ( 5297) covalent geometry : angle 0.57365 ( 7200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8648 (mt) cc_final: 0.8325 (mp) REVERT: A 75 PHE cc_start: 0.5221 (m-80) cc_final: 0.4954 (m-80) REVERT: B 31 ASP cc_start: 0.7943 (t0) cc_final: 0.7589 (t70) REVERT: B 110 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7617 (pt0) REVERT: C 100 LEU cc_start: 0.7517 (tt) cc_final: 0.7118 (tt) REVERT: C 110 HIS cc_start: 0.6142 (OUTLIER) cc_final: 0.5827 (m-70) outliers start: 22 outliers final: 19 residues processed: 51 average time/residue: 0.1492 time to fit residues: 10.6452 Evaluate side-chains 46 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 25 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 36 optimal weight: 0.0170 chunk 62 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.097968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.083757 restraints weight = 18925.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.085582 restraints weight = 12613.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086864 restraints weight = 9350.500| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5298 Z= 0.098 Angle : 0.570 8.422 7202 Z= 0.285 Chirality : 0.041 0.124 800 Planarity : 0.004 0.044 928 Dihedral : 4.847 34.109 715 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.43 % Allowed : 26.76 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.32), residues: 659 helix: 0.15 (0.49), residues: 117 sheet: -2.24 (0.38), residues: 163 loop : -1.59 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 102 HIS 0.006 0.001 HIS C 51 PHE 0.012 0.001 PHE A 75 TYR 0.011 0.001 TYR B 181 ARG 0.002 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 127) hydrogen bonds : angle 5.53192 ( 357) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.44273 ( 2) covalent geometry : bond 0.00230 ( 5297) covalent geometry : angle 0.57028 ( 7200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.51 seconds wall clock time: 34 minutes 20.38 seconds (2060.38 seconds total)