Starting phenix.real_space_refine on Wed Mar 5 14:50:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mqh_48524/03_2025/9mqh_48524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mqh_48524/03_2025/9mqh_48524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mqh_48524/03_2025/9mqh_48524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mqh_48524/03_2025/9mqh_48524.map" model { file = "/net/cci-nas-00/data/ceres_data/9mqh_48524/03_2025/9mqh_48524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mqh_48524/03_2025/9mqh_48524.cif" } resolution = 3.9 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= 0.037 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 1379 2.51 5 N 329 2.21 5 O 345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2074 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2074 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 9, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 106 Time building chain proxies: 3.30, per 1000 atoms: 1.59 Number of scatterers: 2074 At special positions: 0 Unit cell: (64.295, 57.615, 78.49, 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 345 8.00 N 329 7.00 C 1379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 219 " 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 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 248.7 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 1 sheets defined 87.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 72 through 97 removed outlier: 3.914A pdb=" N LEU A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 96 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.535A pdb=" N LYS A 102 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.690A pdb=" N ILE A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 removed outlier: 3.878A pdb=" N ASN A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 173 removed outlier: 3.883A pdb=" N MET A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.070A pdb=" N ASP A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 187 through 208 removed outlier: 3.980A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.505A pdb=" N ALA A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.855A pdb=" N LYS A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 270 through 309 removed outlier: 4.230A pdb=" N ARG A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.598A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 338 removed outlier: 3.864A pdb=" N ASN A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.708A pdb=" N ARG A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 212 162 hydrogen bonds defined for protein. 480 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: 0.58 Time building geometry restraints manager: 0.67 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: 624 1.35 - 1.46: 544 1.46 - 1.58: 926 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 2124 Sorted by residual: bond pdb=" CG LEU A 202 " pdb=" CD2 LEU A 202 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.03e-01 bond pdb=" C PHE A 137 " pdb=" N GLY A 138 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 4.80e-01 bond pdb=" CB ILE A 169 " pdb=" CG2 ILE A 169 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.56e-01 bond pdb=" CG MET A 257 " pdb=" SD MET A 257 " ideal model delta sigma weight residual 1.803 1.788 0.015 2.50e-02 1.60e+03 3.63e-01 bond pdb=" C LEU A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.25e-01 ... (remaining 2119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 2800 1.24 - 2.48: 91 2.48 - 3.73: 14 3.73 - 4.97: 8 4.97 - 6.21: 2 Bond angle restraints: 2915 Sorted by residual: angle pdb=" N MET A 132 " pdb=" CA MET A 132 " pdb=" C MET A 132 " ideal model delta sigma weight residual 113.43 110.58 2.85 1.26e+00 6.30e-01 5.13e+00 angle pdb=" CA GLY A 138 " pdb=" C GLY A 138 " pdb=" N THR A 139 " ideal model delta sigma weight residual 115.34 117.01 -1.67 8.40e-01 1.42e+00 3.93e+00 angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 122.51 -6.21 3.50e+00 8.16e-02 3.15e+00 angle pdb=" CB MET A 207 " pdb=" CG MET A 207 " pdb=" SD MET A 207 " ideal model delta sigma weight residual 112.70 117.75 -5.05 3.00e+00 1.11e-01 2.84e+00 angle pdb=" CA GLY A 138 " pdb=" C GLY A 138 " pdb=" O GLY A 138 " ideal model delta sigma weight residual 122.14 120.41 1.73 1.05e+00 9.07e-01 2.70e+00 ... (remaining 2910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 1010 12.00 - 24.00: 127 24.00 - 35.99: 62 35.99 - 47.99: 23 47.99 - 59.99: 5 Dihedral angle restraints: 1227 sinusoidal: 393 harmonic: 834 Sorted by residual: dihedral pdb=" CA PHE A 243 " pdb=" C PHE A 243 " pdb=" N ILE A 244 " pdb=" CA ILE A 244 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CA ILE A 107 " pdb=" CB ILE A 107 " pdb=" CG1 ILE A 107 " pdb=" CD1 ILE A 107 " ideal model delta sinusoidal sigma weight residual 180.00 120.01 59.99 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N TYR A 130 " pdb=" CA TYR A 130 " pdb=" CB TYR A 130 " pdb=" CG TYR A 130 " ideal model delta sinusoidal sigma weight residual -60.00 -115.46 55.46 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 1224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 224 0.030 - 0.060: 96 0.060 - 0.090: 34 0.090 - 0.120: 10 0.120 - 0.149: 4 Chirality restraints: 368 Sorted by residual: chirality pdb=" CA LEU A 202 " pdb=" N LEU A 202 " pdb=" C LEU A 202 " pdb=" CB LEU A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE A 310 " pdb=" N ILE A 310 " pdb=" C ILE A 310 " pdb=" CB ILE A 310 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CB THR A 155 " pdb=" CA THR A 155 " pdb=" OG1 THR A 155 " pdb=" CG2 THR A 155 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 365 not shown) Planarity restraints: 352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 151 " 0.005 2.00e-02 2.50e+03 9.68e-03 9.37e-01 pdb=" C TYR A 151 " -0.017 2.00e-02 2.50e+03 pdb=" O TYR A 151 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN A 152 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 173 " -0.014 5.00e-02 4.00e+02 2.12e-02 7.21e-01 pdb=" N PRO A 174 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 334 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.28e-01 pdb=" N PRO A 335 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.011 5.00e-02 4.00e+02 ... (remaining 349 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 267 2.74 - 3.28: 2118 3.28 - 3.82: 3498 3.82 - 4.36: 3427 4.36 - 4.90: 6293 Nonbonded interactions: 15603 Sorted by model distance: nonbonded pdb=" O GLY A 84 " pdb=" ND2 ASN A 88 " model vdw 2.206 3.120 nonbonded pdb=" O LEU A 118 " pdb=" OG SER A 121 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 122 " pdb=" OE1 GLN A 126 " model vdw 2.249 3.040 nonbonded pdb=" O LEU A 123 " pdb=" OG SER A 127 " model vdw 2.343 3.040 nonbonded pdb=" NE1 TRP A 135 " pdb=" O GLY A 138 " model vdw 2.346 3.120 ... (remaining 15598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.040 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 0.023 2124 Z= 0.201 Angle : 0.588 6.211 2915 Z= 0.317 Chirality : 0.040 0.149 368 Planarity : 0.003 0.026 352 Dihedral : 15.160 59.987 680 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.92 % Allowed : 26.47 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.53), residues: 277 helix: 1.72 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -1.44 (0.86), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 295 HIS 0.002 0.001 HIS A 299 PHE 0.007 0.001 PHE A 243 TYR 0.011 0.001 TYR A 130 ARG 0.002 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 130 TYR cc_start: 0.4392 (OUTLIER) cc_final: 0.3633 (t80) REVERT: A 140 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7793 (tt) REVERT: A 189 ILE cc_start: 0.8809 (mm) cc_final: 0.8431 (mm) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.0790 time to fit residues: 5.4079 Evaluate side-chains 55 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 310 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124433 restraints weight = 3924.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127105 restraints weight = 2121.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128779 restraints weight = 1443.753| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2124 Z= 0.229 Angle : 0.567 5.042 2915 Z= 0.301 Chirality : 0.041 0.146 368 Planarity : 0.004 0.031 352 Dihedral : 7.458 58.176 309 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 8.82 % Allowed : 21.08 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.53), residues: 277 helix: 2.00 (0.35), residues: 214 sheet: None (None), residues: 0 loop : -1.67 (0.89), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 320 HIS 0.002 0.001 HIS A 299 PHE 0.019 0.001 PHE A 89 TYR 0.011 0.001 TYR A 130 ARG 0.002 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7892 (mtp) REVERT: A 130 TYR cc_start: 0.4238 (OUTLIER) cc_final: 0.3280 (t80) REVERT: A 140 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7797 (tt) REVERT: A 189 ILE cc_start: 0.8856 (mm) cc_final: 0.8491 (mm) REVERT: A 207 MET cc_start: 0.8469 (mpp) cc_final: 0.8125 (mpp) REVERT: A 331 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 332 CYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7977 (t) outliers start: 18 outliers final: 9 residues processed: 64 average time/residue: 0.0920 time to fit residues: 7.5230 Evaluate side-chains 61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 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 = 0.3813 r_free = 0.3813 target = 0.144276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124434 restraints weight = 3926.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126956 restraints weight = 2140.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128860 restraints weight = 1473.711| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2124 Z= 0.221 Angle : 0.543 4.921 2915 Z= 0.289 Chirality : 0.040 0.132 368 Planarity : 0.003 0.022 352 Dihedral : 7.255 58.658 306 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 9.31 % Allowed : 21.08 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.53), residues: 277 helix: 2.08 (0.35), residues: 214 sheet: None (None), residues: 0 loop : -1.62 (0.89), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 320 HIS 0.002 0.001 HIS A 299 PHE 0.006 0.001 PHE A 158 TYR 0.010 0.001 TYR A 130 ARG 0.005 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7816 (mtp) REVERT: A 130 TYR cc_start: 0.4223 (OUTLIER) cc_final: 0.3058 (t80) REVERT: A 140 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 189 ILE cc_start: 0.8865 (mm) cc_final: 0.8502 (mm) REVERT: A 207 MET cc_start: 0.8452 (mpp) cc_final: 0.8169 (mpp) REVERT: A 331 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8500 (p) REVERT: A 338 TYR cc_start: 0.8648 (m-10) cc_final: 0.8246 (m-10) outliers start: 19 outliers final: 10 residues processed: 61 average time/residue: 0.0714 time to fit residues: 5.9017 Evaluate side-chains 60 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124468 restraints weight = 3975.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.126898 restraints weight = 2136.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128820 restraints weight = 1484.949| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2124 Z= 0.226 Angle : 0.546 5.094 2915 Z= 0.290 Chirality : 0.040 0.148 368 Planarity : 0.003 0.023 352 Dihedral : 6.370 49.652 305 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 9.31 % Allowed : 22.55 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.53), residues: 277 helix: 2.20 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -1.29 (0.91), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 320 HIS 0.002 0.001 HIS A 299 PHE 0.006 0.001 PHE A 158 TYR 0.011 0.001 TYR A 130 ARG 0.004 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7767 (mtp) REVERT: A 130 TYR cc_start: 0.3843 (OUTLIER) cc_final: 0.2710 (t80) REVERT: A 140 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7699 (tt) REVERT: A 189 ILE cc_start: 0.8881 (mm) cc_final: 0.8503 (mm) REVERT: A 207 MET cc_start: 0.8461 (mpp) cc_final: 0.8219 (mpp) REVERT: A 331 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 338 TYR cc_start: 0.8645 (m-10) cc_final: 0.8233 (m-10) outliers start: 19 outliers final: 13 residues processed: 61 average time/residue: 0.0696 time to fit residues: 5.7216 Evaluate side-chains 63 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 331 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 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 = 0.3850 r_free = 0.3850 target = 0.147990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128021 restraints weight = 4034.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130882 restraints weight = 2153.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132185 restraints weight = 1461.142| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2124 Z= 0.148 Angle : 0.491 4.764 2915 Z= 0.265 Chirality : 0.039 0.161 368 Planarity : 0.003 0.020 352 Dihedral : 6.132 45.023 305 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 7.84 % Allowed : 26.47 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.54), residues: 277 helix: 2.35 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -0.98 (0.93), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 320 HIS 0.001 0.000 HIS A 299 PHE 0.011 0.001 PHE A 89 TYR 0.011 0.001 TYR A 254 ARG 0.003 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7741 (mtp) REVERT: A 130 TYR cc_start: 0.3825 (OUTLIER) cc_final: 0.2821 (t80) REVERT: A 140 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7654 (tt) REVERT: A 189 ILE cc_start: 0.8765 (mm) cc_final: 0.8443 (mm) REVERT: A 207 MET cc_start: 0.8406 (mpp) cc_final: 0.8188 (mpp) REVERT: A 285 LEU cc_start: 0.8551 (tp) cc_final: 0.8322 (tt) REVERT: A 331 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8453 (p) REVERT: A 338 TYR cc_start: 0.8635 (m-10) cc_final: 0.8195 (m-10) outliers start: 16 outliers final: 9 residues processed: 63 average time/residue: 0.0712 time to fit residues: 6.1166 Evaluate side-chains 62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 331 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126936 restraints weight = 3981.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129700 restraints weight = 2143.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131381 restraints weight = 1454.313| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2124 Z= 0.188 Angle : 0.523 4.899 2915 Z= 0.277 Chirality : 0.039 0.145 368 Planarity : 0.003 0.019 352 Dihedral : 6.075 43.726 305 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.37 % Allowed : 26.96 % Favored : 66.67 % 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: 2.26 (0.53), residues: 277 helix: 2.28 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -1.12 (0.90), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 320 HIS 0.002 0.001 HIS A 299 PHE 0.008 0.001 PHE A 89 TYR 0.009 0.001 TYR A 254 ARG 0.004 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7787 (mtp) REVERT: A 140 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7700 (tt) REVERT: A 189 ILE cc_start: 0.8797 (mm) cc_final: 0.8470 (mm) REVERT: A 207 MET cc_start: 0.8383 (mpp) cc_final: 0.8148 (mpp) REVERT: A 338 TYR cc_start: 0.8656 (m-10) cc_final: 0.8217 (m-10) outliers start: 13 outliers final: 11 residues processed: 57 average time/residue: 0.0682 time to fit residues: 5.2370 Evaluate side-chains 60 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127623 restraints weight = 4077.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130491 restraints weight = 2162.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132052 restraints weight = 1459.038| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2124 Z= 0.191 Angle : 0.537 6.306 2915 Z= 0.282 Chirality : 0.040 0.138 368 Planarity : 0.003 0.019 352 Dihedral : 5.584 43.305 303 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.37 % Allowed : 28.43 % Favored : 65.20 % 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 (0.53), residues: 277 helix: 2.20 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.45 (0.92), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 320 HIS 0.002 0.001 HIS A 299 PHE 0.022 0.001 PHE A 89 TYR 0.009 0.001 TYR A 254 ARG 0.003 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7781 (mtp) REVERT: A 140 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 189 ILE cc_start: 0.8812 (mm) cc_final: 0.8481 (mm) REVERT: A 207 MET cc_start: 0.8420 (mpp) cc_final: 0.8192 (mpp) REVERT: A 338 TYR cc_start: 0.8664 (m-10) cc_final: 0.8242 (m-10) outliers start: 13 outliers final: 10 residues processed: 55 average time/residue: 0.0730 time to fit residues: 5.3936 Evaluate side-chains 58 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.0060 chunk 3 optimal weight: 0.7980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129386 restraints weight = 4115.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132332 restraints weight = 2173.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134118 restraints weight = 1457.697| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2124 Z= 0.150 Angle : 0.514 6.385 2915 Z= 0.270 Chirality : 0.039 0.131 368 Planarity : 0.003 0.018 352 Dihedral : 5.470 43.409 303 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.37 % Allowed : 28.43 % Favored : 65.20 % 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: 2.34 (0.53), residues: 277 helix: 2.32 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -1.47 (0.93), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 320 HIS 0.001 0.000 HIS A 299 PHE 0.004 0.001 PHE A 89 TYR 0.013 0.001 TYR A 254 ARG 0.003 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7794 (mtp) REVERT: A 140 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7748 (tp) REVERT: A 189 ILE cc_start: 0.8740 (mm) cc_final: 0.8413 (mm) REVERT: A 338 TYR cc_start: 0.8629 (m-10) cc_final: 0.8231 (m-10) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.0692 time to fit residues: 5.2459 Evaluate side-chains 58 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128074 restraints weight = 4069.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130908 restraints weight = 2179.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132853 restraints weight = 1471.989| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2124 Z= 0.178 Angle : 0.537 5.775 2915 Z= 0.282 Chirality : 0.040 0.128 368 Planarity : 0.003 0.018 352 Dihedral : 5.489 43.106 303 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.88 % Allowed : 29.41 % Favored : 64.71 % 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: 2.32 (0.53), residues: 277 helix: 2.31 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -1.50 (0.92), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 320 HIS 0.002 0.001 HIS A 299 PHE 0.012 0.001 PHE A 89 TYR 0.012 0.001 TYR A 254 ARG 0.003 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7749 (tp) REVERT: A 189 ILE cc_start: 0.8755 (mm) cc_final: 0.8442 (mm) REVERT: A 207 MET cc_start: 0.8445 (mpp) cc_final: 0.8061 (mpp) REVERT: A 331 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8429 (p) REVERT: A 338 TYR cc_start: 0.8649 (m-10) cc_final: 0.8196 (m-10) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 0.0675 time to fit residues: 4.9105 Evaluate side-chains 57 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125343 restraints weight = 4088.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128099 restraints weight = 2200.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129666 restraints weight = 1492.741| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2124 Z= 0.242 Angle : 0.573 5.571 2915 Z= 0.305 Chirality : 0.041 0.139 368 Planarity : 0.003 0.022 352 Dihedral : 5.687 42.568 303 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.90 % Allowed : 29.90 % Favored : 65.20 % 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: 2.12 (0.53), residues: 277 helix: 2.25 (0.35), residues: 214 sheet: None (None), residues: 0 loop : -1.71 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 320 HIS 0.003 0.001 HIS A 299 PHE 0.007 0.001 PHE A 158 TYR 0.013 0.001 TYR A 130 ARG 0.003 0.001 ARG A 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7638 (tt) REVERT: A 189 ILE cc_start: 0.8880 (mm) cc_final: 0.8498 (mm) REVERT: A 285 LEU cc_start: 0.8506 (tp) cc_final: 0.8171 (tt) REVERT: A 338 TYR cc_start: 0.8638 (m-10) cc_final: 0.8184 (m-10) outliers start: 10 outliers final: 9 residues processed: 50 average time/residue: 0.0725 time to fit residues: 4.9003 Evaluate side-chains 55 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 9 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.127969 restraints weight = 4086.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130680 restraints weight = 2192.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132671 restraints weight = 1491.918| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2124 Z= 0.166 Angle : 0.526 5.357 2915 Z= 0.278 Chirality : 0.039 0.133 368 Planarity : 0.003 0.018 352 Dihedral : 5.549 43.036 303 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.88 % Allowed : 28.92 % Favored : 65.20 % 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: 2.34 (0.53), residues: 277 helix: 2.35 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.49 (0.89), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 320 HIS 0.001 0.000 HIS A 299 PHE 0.035 0.001 PHE A 89 TYR 0.009 0.001 TYR A 254 ARG 0.003 0.001 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1178.31 seconds wall clock time: 21 minutes 2.11 seconds (1262.11 seconds total)