Starting phenix.real_space_refine on Tue Jul 29 04:32:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tlu_41373/07_2025/8tlu_41373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tlu_41373/07_2025/8tlu_41373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tlu_41373/07_2025/8tlu_41373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tlu_41373/07_2025/8tlu_41373.map" model { file = "/net/cci-nas-00/data/ceres_data/8tlu_41373/07_2025/8tlu_41373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tlu_41373/07_2025/8tlu_41373.cif" } resolution = 3.8 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= 1.000 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: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 3689 2.51 5 N 885 2.21 5 O 873 1.98 5 H 5703 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5606 Classifications: {'peptide': 350} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 335} Chain breaks: 2 Chain: "E" Number of atoms: 5574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5574 Classifications: {'peptide': 348} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain breaks: 2 Time building chain proxies: 5.92, per 1000 atoms: 0.53 Number of scatterers: 11180 At special positions: 0 Unit cell: (79.872, 93.184, 74.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 873 8.00 N 885 7.00 C 3689 6.00 H 5703 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.16 Conformation dependent library (CDL) restraints added in 786.5 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.007A pdb=" N VAL A 18 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 53 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 95 through 121 removed outlier: 4.044A pdb=" N TRP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 152 Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.761A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 4.067A pdb=" N ASN A 221 " --> pdb=" O TRP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 238 through 256 removed outlier: 3.663A pdb=" N VAL A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 285 removed outlier: 6.029A pdb=" N ALA A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 334 through 359 removed outlier: 3.747A pdb=" N ILE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.513A pdb=" N PHE E 16 " --> pdb=" O TYR E 13 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 18 " --> pdb=" O GLY E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 Processing helix chain 'E' and resid 41 through 54 Processing helix chain 'E' and resid 75 through 91 removed outlier: 3.965A pdb=" N ILE E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 removed outlier: 3.672A pdb=" N TRP E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 152 Processing helix chain 'E' and resid 155 through 159 removed outlier: 3.696A pdb=" N GLN E 159 " --> pdb=" O PRO E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 195 removed outlier: 3.964A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 221 removed outlier: 3.775A pdb=" N ASN E 221 " --> pdb=" O TRP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 229 Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 238 through 255 removed outlier: 3.930A pdb=" N VAL E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 284 removed outlier: 4.130A pdb=" N GLY E 269 " --> pdb=" O MET E 265 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'E' and resid 323 through 332 Processing helix chain 'E' and resid 334 through 360 removed outlier: 3.562A pdb=" N LEU E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 360 " --> pdb=" O THR E 356 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1167 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: 3.95 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5699 1.03 - 1.23: 4 1.23 - 1.42: 2378 1.42 - 1.61: 3199 1.61 - 1.81: 56 Bond restraints: 11336 Sorted by residual: bond pdb=" CG LEU E 283 " pdb=" CD1 LEU E 283 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB THR A 244 " pdb=" CG2 THR A 244 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.67e-01 bond pdb=" CB THR E 244 " pdb=" CG2 THR E 244 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" CB ASP E 195 " pdb=" CG ASP E 195 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.18e-01 bond pdb=" CB MET A 348 " pdb=" CG MET A 348 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.08e-01 ... (remaining 11331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 20171 1.54 - 3.09: 341 3.09 - 4.63: 31 4.63 - 6.17: 3 6.17 - 7.72: 2 Bond angle restraints: 20548 Sorted by residual: angle pdb=" CB MET E 222 " pdb=" CG MET E 222 " pdb=" SD MET E 222 " ideal model delta sigma weight residual 112.70 120.42 -7.72 3.00e+00 1.11e-01 6.62e+00 angle pdb=" CA LEU E 34 " pdb=" CB LEU E 34 " pdb=" CG LEU E 34 " ideal model delta sigma weight residual 116.30 108.73 7.57 3.50e+00 8.16e-02 4.68e+00 angle pdb=" C ALA A 130 " pdb=" N ARG A 131 " pdb=" CA ARG A 131 " ideal model delta sigma weight residual 121.54 125.03 -3.49 1.91e+00 2.74e-01 3.33e+00 angle pdb=" C TYR A 328 " pdb=" N GLU A 329 " pdb=" CA GLU A 329 " ideal model delta sigma weight residual 120.29 117.70 2.59 1.42e+00 4.96e-01 3.33e+00 angle pdb=" N MET A 203 " pdb=" CA MET A 203 " pdb=" C MET A 203 " ideal model delta sigma weight residual 113.16 110.59 2.57 1.42e+00 4.96e-01 3.27e+00 ... (remaining 20543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 4397 11.96 - 23.92: 549 23.92 - 35.88: 184 35.88 - 47.84: 70 47.84 - 59.79: 85 Dihedral angle restraints: 5285 sinusoidal: 2775 harmonic: 2510 Sorted by residual: dihedral pdb=" CA TYR A 21 " pdb=" C TYR A 21 " pdb=" N LEU A 22 " pdb=" CA LEU A 22 " ideal model delta harmonic sigma weight residual -180.00 -160.04 -19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS A 8 " pdb=" C HIS A 8 " pdb=" N LEU A 9 " pdb=" CA LEU A 9 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA TYR E 259 " pdb=" C TYR E 259 " pdb=" N PRO E 260 " pdb=" CA PRO E 260 " ideal model delta harmonic sigma weight residual 180.00 164.38 15.62 0 5.00e+00 4.00e-02 9.76e+00 ... (remaining 5282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 568 0.029 - 0.058: 212 0.058 - 0.087: 85 0.087 - 0.116: 25 0.116 - 0.145: 4 Chirality restraints: 894 Sorted by residual: chirality pdb=" CA ILE E 230 " pdb=" N ILE E 230 " pdb=" C ILE E 230 " pdb=" CB ILE E 230 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA PRO E 156 " pdb=" N PRO E 156 " pdb=" C PRO E 156 " pdb=" CB PRO E 156 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 891 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 259 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO A 260 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 260 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 260 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 131 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ARG A 131 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG A 131 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP A 132 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 230 " -0.019 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO A 231 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.016 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 760 2.21 - 2.81: 23701 2.81 - 3.40: 32167 3.40 - 4.00: 40703 4.00 - 4.60: 63626 Nonbonded interactions: 160957 Sorted by model distance: nonbonded pdb=" HG SER E 303 " pdb=" O ALA E 322 " model vdw 1.610 2.450 nonbonded pdb=" H3 MET E 1 " pdb=" O LEU E 88 " model vdw 1.638 2.450 nonbonded pdb=" OD1 ASP A 124 " pdb=" H THR A 125 " model vdw 1.645 2.450 nonbonded pdb="HH21 ARG A 337 " pdb=" O PRO E 260 " model vdw 1.671 2.450 nonbonded pdb=" O ALA E 190 " pdb=" HG1 THR E 194 " model vdw 1.680 2.450 ... (remaining 160952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 121 or resid 129 through 360)) selection = (chain 'E' and (resid 1 through 56 or resid 64 through 360)) } 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: 0.640 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: 0.210 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.850 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 0.042 5633 Z= 0.145 Angle : 0.536 7.718 7674 Z= 0.287 Chirality : 0.037 0.145 894 Planarity : 0.004 0.057 921 Dihedral : 12.886 58.139 1926 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.57 (0.32), residues: 686 helix: 1.52 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -0.36 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 132 HIS 0.009 0.001 HIS A 8 PHE 0.017 0.001 PHE A 164 TYR 0.016 0.001 TYR A 21 ARG 0.002 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.09834 ( 395) hydrogen bonds : angle 5.03233 ( 1167) covalent geometry : bond 0.00325 ( 5633) covalent geometry : angle 0.53558 ( 7674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8558 (mt) cc_final: 0.8197 (mt) REVERT: A 203 MET cc_start: 0.7984 (tpt) cc_final: 0.6916 (tpt) REVERT: A 232 TYR cc_start: 0.7995 (t80) cc_final: 0.7615 (t80) REVERT: E 203 MET cc_start: 0.7476 (tpt) cc_final: 0.7066 (tpt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3023 time to fit residues: 55.4370 Evaluate side-chains 124 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.165714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.144457 restraints weight = 17962.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.144985 restraints weight = 14222.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.145280 restraints weight = 12818.435| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5633 Z= 0.163 Angle : 0.528 6.500 7674 Z= 0.282 Chirality : 0.037 0.142 894 Planarity : 0.004 0.042 921 Dihedral : 3.805 16.513 752 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.87 % Allowed : 5.07 % Favored : 94.06 % 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: 1.43 (0.32), residues: 686 helix: 1.42 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.41 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.006 0.001 HIS A 8 PHE 0.011 0.001 PHE A 164 TYR 0.012 0.001 TYR A 176 ARG 0.003 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 395) hydrogen bonds : angle 4.43110 ( 1167) covalent geometry : bond 0.00375 ( 5633) covalent geometry : angle 0.52827 ( 7674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9315 (t) cc_final: 0.9080 (p) REVERT: A 232 TYR cc_start: 0.8022 (t80) cc_final: 0.7569 (t80) REVERT: E 203 MET cc_start: 0.7766 (tpt) cc_final: 0.7396 (tpt) outliers start: 5 outliers final: 4 residues processed: 126 average time/residue: 0.3435 time to fit residues: 58.3678 Evaluate side-chains 118 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 0.0270 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.167703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.144924 restraints weight = 17924.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.148298 restraints weight = 12374.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.151079 restraints weight = 9469.823| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5633 Z= 0.116 Angle : 0.483 4.888 7674 Z= 0.254 Chirality : 0.036 0.150 894 Planarity : 0.004 0.037 921 Dihedral : 3.675 16.038 752 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.75 % Allowed : 6.82 % Favored : 91.43 % 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: 1.60 (0.32), residues: 686 helix: 1.56 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.43 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 99 HIS 0.005 0.001 HIS A 8 PHE 0.008 0.001 PHE A 66 TYR 0.008 0.001 TYR A 176 ARG 0.001 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 395) hydrogen bonds : angle 4.20945 ( 1167) covalent geometry : bond 0.00257 ( 5633) covalent geometry : angle 0.48328 ( 7674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.4023 (OUTLIER) cc_final: 0.2888 (p90) REVERT: A 106 VAL cc_start: 0.9298 (t) cc_final: 0.9068 (p) REVERT: E 203 MET cc_start: 0.7732 (tpt) cc_final: 0.7339 (tpt) outliers start: 10 outliers final: 8 residues processed: 121 average time/residue: 0.3264 time to fit residues: 55.2461 Evaluate side-chains 124 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.167652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.145322 restraints weight = 17608.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.148616 restraints weight = 12280.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.151402 restraints weight = 9445.796| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5633 Z= 0.115 Angle : 0.475 4.760 7674 Z= 0.250 Chirality : 0.036 0.144 894 Planarity : 0.004 0.044 921 Dihedral : 3.621 16.146 752 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.40 % Allowed : 7.69 % Favored : 90.91 % 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: 1.73 (0.32), residues: 686 helix: 1.66 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.38 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 PHE 0.008 0.001 PHE A 66 TYR 0.009 0.001 TYR A 176 ARG 0.001 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 395) hydrogen bonds : angle 4.12563 ( 1167) covalent geometry : bond 0.00256 ( 5633) covalent geometry : angle 0.47463 ( 7674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3911 (OUTLIER) cc_final: 0.2357 (p90) REVERT: A 106 VAL cc_start: 0.9294 (t) cc_final: 0.9066 (p) REVERT: A 181 TYR cc_start: 0.8519 (t80) cc_final: 0.8289 (t80) REVERT: E 203 MET cc_start: 0.7724 (tpt) cc_final: 0.7265 (tpt) REVERT: E 222 MET cc_start: 0.6055 (mmp) cc_final: 0.5759 (mmp) REVERT: E 271 LEU cc_start: 0.9020 (mt) cc_final: 0.8774 (mp) outliers start: 8 outliers final: 6 residues processed: 127 average time/residue: 0.3279 time to fit residues: 58.4327 Evaluate side-chains 124 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.0050 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.163680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.140840 restraints weight = 17880.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.143978 restraints weight = 12627.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.146590 restraints weight = 9847.286| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5633 Z= 0.159 Angle : 0.506 5.085 7674 Z= 0.271 Chirality : 0.037 0.141 894 Planarity : 0.004 0.045 921 Dihedral : 3.683 16.638 752 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.75 % Allowed : 8.57 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.32), residues: 686 helix: 1.54 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.49 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 PHE 0.010 0.001 PHE E 253 TYR 0.011 0.001 TYR A 176 ARG 0.003 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 395) hydrogen bonds : angle 4.22664 ( 1167) covalent geometry : bond 0.00367 ( 5633) covalent geometry : angle 0.50560 ( 7674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3910 (OUTLIER) cc_final: 0.2325 (p90) REVERT: A 181 TYR cc_start: 0.8576 (t80) cc_final: 0.8294 (t80) REVERT: A 195 ASP cc_start: 0.8337 (t70) cc_final: 0.8135 (t70) REVERT: E 222 MET cc_start: 0.6263 (mmp) cc_final: 0.5984 (mmp) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.2937 time to fit residues: 55.0505 Evaluate side-chains 134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.166665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.144129 restraints weight = 17798.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.147597 restraints weight = 12345.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.149936 restraints weight = 9466.306| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5633 Z= 0.109 Angle : 0.477 4.857 7674 Z= 0.249 Chirality : 0.036 0.141 894 Planarity : 0.004 0.046 921 Dihedral : 3.606 16.335 752 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.40 % Allowed : 10.49 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.32), residues: 686 helix: 1.75 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.40 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 99 HIS 0.004 0.001 HIS A 8 PHE 0.007 0.001 PHE A 66 TYR 0.009 0.001 TYR A 176 ARG 0.002 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 395) hydrogen bonds : angle 4.09000 ( 1167) covalent geometry : bond 0.00237 ( 5633) covalent geometry : angle 0.47665 ( 7674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3889 (OUTLIER) cc_final: 0.2296 (p90) REVERT: A 106 VAL cc_start: 0.9309 (t) cc_final: 0.9098 (p) REVERT: A 181 TYR cc_start: 0.8535 (t80) cc_final: 0.8216 (t80) REVERT: A 195 ASP cc_start: 0.8294 (t70) cc_final: 0.7978 (t70) outliers start: 8 outliers final: 7 residues processed: 126 average time/residue: 0.3025 time to fit residues: 52.8614 Evaluate side-chains 129 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.163076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.140070 restraints weight = 18146.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.143399 restraints weight = 12804.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.145602 restraints weight = 10040.499| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5633 Z= 0.161 Angle : 0.516 5.009 7674 Z= 0.274 Chirality : 0.036 0.142 894 Planarity : 0.004 0.046 921 Dihedral : 3.704 17.079 752 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.57 % Allowed : 10.31 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.32), residues: 686 helix: 1.60 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.51 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 PHE 0.010 0.001 PHE E 253 TYR 0.008 0.001 TYR A 176 ARG 0.002 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 395) hydrogen bonds : angle 4.22311 ( 1167) covalent geometry : bond 0.00373 ( 5633) covalent geometry : angle 0.51598 ( 7674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3958 (OUTLIER) cc_final: 0.2343 (p90) REVERT: A 181 TYR cc_start: 0.8575 (t80) cc_final: 0.8248 (t80) REVERT: A 195 ASP cc_start: 0.8395 (t70) cc_final: 0.8115 (t70) outliers start: 9 outliers final: 7 residues processed: 128 average time/residue: 0.3488 time to fit residues: 60.1838 Evaluate side-chains 131 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.165282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.142745 restraints weight = 17772.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.145899 restraints weight = 12455.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.148780 restraints weight = 9691.068| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5633 Z= 0.121 Angle : 0.492 4.977 7674 Z= 0.257 Chirality : 0.036 0.145 894 Planarity : 0.004 0.048 921 Dihedral : 3.641 16.415 752 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.22 % Allowed : 11.36 % Favored : 87.41 % 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: 1.79 (0.32), residues: 686 helix: 1.73 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.49 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 99 HIS 0.003 0.001 HIS A 8 PHE 0.006 0.001 PHE A 66 TYR 0.006 0.001 TYR A 176 ARG 0.002 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 395) hydrogen bonds : angle 4.13158 ( 1167) covalent geometry : bond 0.00272 ( 5633) covalent geometry : angle 0.49175 ( 7674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3932 (OUTLIER) cc_final: 0.2353 (p90) REVERT: A 106 VAL cc_start: 0.9295 (t) cc_final: 0.9062 (p) REVERT: A 181 TYR cc_start: 0.8529 (t80) cc_final: 0.8180 (t80) REVERT: A 195 ASP cc_start: 0.8354 (t70) cc_final: 0.8059 (t70) outliers start: 7 outliers final: 6 residues processed: 125 average time/residue: 0.3557 time to fit residues: 62.0488 Evaluate side-chains 127 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.166956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.144727 restraints weight = 17789.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.147833 restraints weight = 12343.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.150558 restraints weight = 9573.094| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5633 Z= 0.111 Angle : 0.483 5.225 7674 Z= 0.251 Chirality : 0.036 0.156 894 Planarity : 0.004 0.050 921 Dihedral : 3.579 16.639 752 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.40 % Allowed : 11.36 % Favored : 87.24 % 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: 1.91 (0.32), residues: 686 helix: 1.83 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.48 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 132 HIS 0.003 0.001 HIS A 8 PHE 0.006 0.001 PHE A 66 TYR 0.011 0.001 TYR A 21 ARG 0.001 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 395) hydrogen bonds : angle 4.05303 ( 1167) covalent geometry : bond 0.00246 ( 5633) covalent geometry : angle 0.48320 ( 7674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.3970 (OUTLIER) cc_final: 0.2429 (p90) REVERT: A 106 VAL cc_start: 0.9291 (t) cc_final: 0.9074 (p) REVERT: A 181 TYR cc_start: 0.8514 (t80) cc_final: 0.8142 (t80) REVERT: A 195 ASP cc_start: 0.8319 (t70) cc_final: 0.8103 (t70) REVERT: E 222 MET cc_start: 0.6245 (mmp) cc_final: 0.5787 (mmp) outliers start: 8 outliers final: 7 residues processed: 126 average time/residue: 0.3004 time to fit residues: 52.2957 Evaluate side-chains 128 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 311 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.163236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.140197 restraints weight = 18062.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.143472 restraints weight = 12878.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.146023 restraints weight = 9984.480| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5633 Z= 0.159 Angle : 0.524 5.890 7674 Z= 0.278 Chirality : 0.037 0.146 894 Planarity : 0.004 0.054 921 Dihedral : 3.701 17.272 752 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.40 % Allowed : 11.54 % Favored : 87.06 % 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: 1.65 (0.32), residues: 686 helix: 1.64 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.59 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 39 HIS 0.004 0.001 HIS A 8 PHE 0.009 0.001 PHE E 253 TYR 0.009 0.001 TYR A 259 ARG 0.002 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 395) hydrogen bonds : angle 4.21973 ( 1167) covalent geometry : bond 0.00368 ( 5633) covalent geometry : angle 0.52430 ( 7674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.4020 (OUTLIER) cc_final: 0.2421 (p90) REVERT: A 106 VAL cc_start: 0.9339 (t) cc_final: 0.9116 (p) REVERT: A 181 TYR cc_start: 0.8580 (t80) cc_final: 0.8224 (t80) REVERT: A 195 ASP cc_start: 0.8422 (t70) cc_final: 0.8143 (t70) outliers start: 8 outliers final: 6 residues processed: 125 average time/residue: 0.2998 time to fit residues: 51.8090 Evaluate side-chains 127 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.166494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.143913 restraints weight = 17635.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.147228 restraints weight = 12364.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.149514 restraints weight = 9635.374| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5633 Z= 0.115 Angle : 0.487 6.074 7674 Z= 0.253 Chirality : 0.036 0.148 894 Planarity : 0.004 0.054 921 Dihedral : 3.603 16.528 752 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.40 % Allowed : 11.89 % Favored : 86.71 % 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: 1.90 (0.32), residues: 686 helix: 1.83 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.51 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 132 HIS 0.003 0.001 HIS A 8 PHE 0.006 0.001 PHE A 66 TYR 0.009 0.001 TYR A 21 ARG 0.002 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 395) hydrogen bonds : angle 4.07014 ( 1167) covalent geometry : bond 0.00255 ( 5633) covalent geometry : angle 0.48733 ( 7674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4440.17 seconds wall clock time: 78 minutes 2.03 seconds (4682.03 seconds total)