Starting phenix.real_space_refine on Sat Jul 20 13:18:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/07_2024/8tlu_41373.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/07_2024/8tlu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/07_2024/8tlu_41373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/07_2024/8tlu_41373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/07_2024/8tlu_41373.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/07_2024/8tlu_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 Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 7": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.23, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.04 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.85 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: 3.69 Time building geometry restraints manager: 9.53 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: 99.43 - 106.33: 170 106.33 - 113.24: 13292 113.24 - 120.15: 3735 120.15 - 127.05: 3261 127.05 - 133.96: 90 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 1.850 nonbonded pdb=" H3 MET E 1 " pdb=" O LEU E 88 " model vdw 1.638 1.850 nonbonded pdb=" OD1 ASP A 124 " pdb=" H THR A 125 " model vdw 1.645 1.850 nonbonded pdb="HH21 ARG A 337 " pdb=" O PRO E 260 " model vdw 1.671 1.850 nonbonded pdb=" O ALA E 190 " pdb=" HG1 THR E 194 " model vdw 1.680 1.850 ... (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 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: 7.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.610 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.830 ------------------------------------------------------------------------------- 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= 0.217 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.794 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: 0.3007 time to fit residues: 54.8201 Evaluate side-chains 124 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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: 1.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5633 Z= 0.235 Angle : 0.515 6.642 7674 Z= 0.274 Chirality : 0.037 0.143 894 Planarity : 0.004 0.039 921 Dihedral : 3.778 16.589 752 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.87 % Allowed : 5.42 % Favored : 93.71 % 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: 1.55 (0.32), residues: 686 helix: 1.50 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.31 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 99 HIS 0.006 0.001 HIS A 8 PHE 0.011 0.001 PHE A 164 TYR 0.011 0.001 TYR A 176 ARG 0.002 0.000 ARG A 25 *********************** 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 129 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9249 (t) cc_final: 0.9003 (p) REVERT: A 232 TYR cc_start: 0.8037 (t80) cc_final: 0.7679 (t80) REVERT: E 203 MET cc_start: 0.7575 (tpt) cc_final: 0.7217 (tpt) outliers start: 5 outliers final: 4 residues processed: 125 average time/residue: 0.3030 time to fit residues: 50.8293 Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5633 Z= 0.175 Angle : 0.484 4.849 7674 Z= 0.255 Chirality : 0.036 0.140 894 Planarity : 0.004 0.034 921 Dihedral : 3.660 15.847 752 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.40 % Allowed : 7.17 % 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: 1.69 (0.32), residues: 686 helix: 1.61 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.35 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 0.004 0.000 ARG E 360 *********************** 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 124 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9249 (t) cc_final: 0.9011 (p) REVERT: E 203 MET cc_start: 0.7593 (tpt) cc_final: 0.7206 (tpt) outliers start: 8 outliers final: 7 residues processed: 119 average time/residue: 0.3047 time to fit residues: 49.4150 Evaluate side-chains 120 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP 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 32 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5633 Z= 0.195 Angle : 0.482 5.112 7674 Z= 0.255 Chirality : 0.036 0.150 894 Planarity : 0.004 0.040 921 Dihedral : 3.643 15.994 752 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.57 % Allowed : 8.92 % Favored : 89.51 % 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: 1.65 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.34 (0.50), 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 0.009 0.001 PHE A 66 TYR 0.009 0.001 TYR A 176 ARG 0.002 0.000 ARG E 360 *********************** 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 132 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9260 (t) cc_final: 0.9042 (p) REVERT: A 181 TYR cc_start: 0.8608 (t80) cc_final: 0.8398 (t80) REVERT: E 222 MET cc_start: 0.6378 (mmp) cc_final: 0.6015 (mmp) REVERT: E 271 LEU cc_start: 0.9046 (mt) cc_final: 0.8805 (mp) outliers start: 9 outliers final: 8 residues processed: 124 average time/residue: 0.3179 time to fit residues: 53.3453 Evaluate side-chains 131 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 203 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5633 Z= 0.179 Angle : 0.476 4.774 7674 Z= 0.250 Chirality : 0.036 0.143 894 Planarity : 0.004 0.042 921 Dihedral : 3.614 15.860 752 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.57 % Allowed : 9.27 % Favored : 89.16 % 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: 1.85 (0.32), residues: 686 helix: 1.75 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.36 (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 0.008 0.001 PHE A 66 TYR 0.011 0.001 TYR A 176 ARG 0.001 0.000 ARG E 285 *********************** 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 136 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9247 (t) cc_final: 0.9010 (p) REVERT: A 181 TYR cc_start: 0.8593 (t80) cc_final: 0.8340 (t80) REVERT: E 222 MET cc_start: 0.6393 (mmp) cc_final: 0.6085 (mmp) outliers start: 9 outliers final: 7 residues processed: 128 average time/residue: 0.3046 time to fit residues: 53.9812 Evaluate side-chains 130 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 203 MET 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 39 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5633 Z= 0.235 Angle : 0.497 4.712 7674 Z= 0.266 Chirality : 0.037 0.146 894 Planarity : 0.004 0.043 921 Dihedral : 3.674 16.244 752 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.75 % Allowed : 9.79 % Favored : 88.46 % 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: 1.70 (0.32), residues: 686 helix: 1.64 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.43 (0.50), 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 0.008 0.001 PHE A 66 TYR 0.008 0.001 TYR A 176 ARG 0.002 0.000 ARG E 285 *********************** 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 134 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.4369 (OUTLIER) cc_final: 0.2599 (p90) REVERT: A 106 VAL cc_start: 0.9293 (t) cc_final: 0.9059 (p) REVERT: A 181 TYR cc_start: 0.8623 (t80) cc_final: 0.8359 (t80) REVERT: A 219 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7925 (m) REVERT: E 222 MET cc_start: 0.6566 (mmp) cc_final: 0.6243 (mmp) outliers start: 10 outliers final: 7 residues processed: 128 average time/residue: 0.3093 time to fit residues: 53.9021 Evaluate side-chains 129 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 203 MET Chi-restraints excluded: chain A residue 219 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5633 Z= 0.142 Angle : 0.471 4.801 7674 Z= 0.244 Chirality : 0.036 0.141 894 Planarity : 0.004 0.043 921 Dihedral : 3.542 15.369 752 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.40 % Allowed : 11.01 % Favored : 87.59 % 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: 2.03 (0.33), residues: 686 helix: 1.89 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -0.35 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 99 HIS 0.003 0.001 HIS A 8 PHE 0.006 0.001 PHE A 66 TYR 0.005 0.001 TYR A 176 ARG 0.002 0.000 ARG A 337 *********************** 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 132 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.4318 (OUTLIER) cc_final: 0.2553 (p90) REVERT: A 106 VAL cc_start: 0.9225 (t) cc_final: 0.8991 (p) REVERT: A 181 TYR cc_start: 0.8588 (t80) cc_final: 0.8280 (t80) REVERT: E 222 MET cc_start: 0.6556 (mmp) cc_final: 0.6272 (mmp) outliers start: 8 outliers final: 6 residues processed: 127 average time/residue: 0.3014 time to fit residues: 52.8692 Evaluate side-chains 126 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5633 Z= 0.180 Angle : 0.484 4.767 7674 Z= 0.253 Chirality : 0.036 0.156 894 Planarity : 0.004 0.043 921 Dihedral : 3.535 15.798 752 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.22 % Allowed : 11.19 % Favored : 87.59 % 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: 2.02 (0.32), residues: 686 helix: 1.88 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.35 (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 0.008 0.001 PHE A 66 TYR 0.006 0.001 TYR A 176 ARG 0.002 0.000 ARG E 285 *********************** 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 127 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.750 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: 0.4320 (OUTLIER) cc_final: 0.2534 (p90) REVERT: A 106 VAL cc_start: 0.9247 (t) cc_final: 0.9024 (p) REVERT: A 181 TYR cc_start: 0.8602 (t80) cc_final: 0.8286 (t80) REVERT: E 222 MET cc_start: 0.6737 (mmp) cc_final: 0.6412 (mmp) outliers start: 7 outliers final: 6 residues processed: 123 average time/residue: 0.3078 time to fit residues: 52.3337 Evaluate side-chains 126 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 26 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 0.0470 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5633 Z= 0.145 Angle : 0.467 4.668 7674 Z= 0.242 Chirality : 0.036 0.141 894 Planarity : 0.004 0.048 921 Dihedral : 3.456 15.171 752 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 2.20 (0.33), residues: 686 helix: 2.01 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -0.27 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 99 HIS 0.003 0.001 HIS A 8 PHE 0.011 0.001 PHE A 66 TYR 0.005 0.001 TYR A 176 ARG 0.001 0.000 ARG E 285 *********************** 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 133 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.796 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: 0.4256 (OUTLIER) cc_final: 0.2521 (p90) REVERT: A 106 VAL cc_start: 0.9214 (t) cc_final: 0.8981 (p) REVERT: A 181 TYR cc_start: 0.8585 (t80) cc_final: 0.8232 (t80) REVERT: A 219 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7526 (m) REVERT: E 222 MET cc_start: 0.6739 (mmp) cc_final: 0.6414 (mmp) outliers start: 8 outliers final: 6 residues processed: 129 average time/residue: 0.2973 time to fit residues: 52.8201 Evaluate side-chains 131 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 219 THR 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 68 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2338 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= 0.198 Angle : 0.491 4.842 7674 Z= 0.258 Chirality : 0.036 0.162 894 Planarity : 0.004 0.050 921 Dihedral : 3.518 16.012 752 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.40 % Allowed : 12.06 % Favored : 86.54 % 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: 2.05 (0.32), residues: 686 helix: 1.89 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.29 (0.52), residues: 165 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 0.013 0.001 PHE A 66 TYR 0.011 0.001 TYR A 21 ARG 0.002 0.000 ARG E 285 ********************** 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 131 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.4347 (OUTLIER) cc_final: 0.2540 (p90) REVERT: A 106 VAL cc_start: 0.9266 (t) cc_final: 0.9050 (p) REVERT: A 181 TYR cc_start: 0.8611 (t80) cc_final: 0.8288 (t80) REVERT: A 219 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7691 (m) REVERT: E 222 MET cc_start: 0.6996 (mmp) cc_final: 0.6642 (mmp) outliers start: 8 outliers final: 5 residues processed: 126 average time/residue: 0.2984 time to fit residues: 51.7973 Evaluate side-chains 129 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 219 THR 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: 0.6980 chunk 54 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.165057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.142170 restraints weight = 17874.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.145400 restraints weight = 12524.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.148003 restraints weight = 9792.000| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5633 Z= 0.220 Angle : 0.499 4.802 7674 Z= 0.264 Chirality : 0.036 0.159 894 Planarity : 0.004 0.051 921 Dihedral : 3.602 15.864 752 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.40 % Allowed : 12.06 % Favored : 86.54 % 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: 1.95 (0.32), residues: 686 helix: 1.82 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.34 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 99 HIS 0.004 0.001 HIS A 8 PHE 0.012 0.001 PHE A 66 TYR 0.010 0.001 TYR A 259 ARG 0.002 0.000 ARG E 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.36 seconds wall clock time: 51 minutes 57.60 seconds (3117.60 seconds total)