Starting phenix.real_space_refine on Sun Aug 4 17:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/08_2024/8tlu_41373.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/08_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_41373/08_2024/8tlu_41373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/08_2024/8tlu_41373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/08_2024/8tlu_41373.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlu_41373/08_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-5409/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: 5.64, per 1000 atoms: 0.50 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: 9.81 Conformation dependent library (CDL) restraints added in 1.1 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: 0.81 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: 3.66 Time building geometry restraints manager: 10.33 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 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: 0.830 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: 0.170 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 39.830 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.470 ------------------------------------------------------------------------------- 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 : 0.820 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: 0.3011 time to fit residues: 54.9157 Evaluate side-chains 124 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1114 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= 0.251 Angle : 0.528 6.501 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9263 (t) cc_final: 0.9021 (p) REVERT: A 232 TYR cc_start: 0.8045 (t80) cc_final: 0.7650 (t80) REVERT: E 203 MET cc_start: 0.7560 (tpt) cc_final: 0.7178 (tpt) outliers start: 5 outliers final: 4 residues processed: 126 average time/residue: 0.3320 time to fit residues: 56.0707 Evaluate side-chains 118 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.1474 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= 0.184 Angle : 0.488 4.988 7674 Z= 0.257 Chirality : 0.036 0.147 894 Planarity : 0.004 0.037 921 Dihedral : 3.692 16.093 752 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.92 % Allowed : 6.64 % 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: 1.55 (0.32), residues: 686 helix: 1.53 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.45 (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 0.009 0.001 PHE A 66 TYR 0.009 0.001 TYR A 176 ARG 0.001 0.000 ARG E 285 *********************** 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 127 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.4151 (OUTLIER) cc_final: 0.3019 (p90) REVERT: A 106 VAL cc_start: 0.9253 (t) cc_final: 0.9025 (p) REVERT: E 203 MET cc_start: 0.7574 (tpt) cc_final: 0.7100 (tpt) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 0.3000 time to fit residues: 48.7643 Evaluate side-chains 124 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.1672 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= 0.195 Angle : 0.486 4.822 7674 Z= 0.257 Chirality : 0.036 0.147 894 Planarity : 0.004 0.044 921 Dihedral : 3.672 16.219 752 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.40 % Allowed : 8.22 % Favored : 90.38 % 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: 1.59 (0.32), residues: 686 helix: 1.57 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.45 (0.49), 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 0.008 0.001 PHE A 66 TYR 0.009 0.001 TYR A 176 ARG 0.002 0.000 ARG E 285 *********************** 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 133 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.917 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: 0.4033 (OUTLIER) cc_final: 0.2468 (p90) REVERT: A 106 VAL cc_start: 0.9272 (t) cc_final: 0.9046 (p) REVERT: E 222 MET cc_start: 0.6310 (mmp) cc_final: 0.5984 (mmp) REVERT: E 271 LEU cc_start: 0.9046 (mt) cc_final: 0.8807 (mp) outliers start: 8 outliers final: 6 residues processed: 126 average time/residue: 0.3063 time to fit residues: 52.8846 Evaluate side-chains 125 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.1817 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= 0.176 Angle : 0.480 5.090 7674 Z= 0.252 Chirality : 0.036 0.142 894 Planarity : 0.004 0.044 921 Dihedral : 3.617 16.123 752 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.40 % Allowed : 8.39 % Favored : 90.21 % 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: 1.74 (0.32), residues: 686 helix: 1.68 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.42 (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 0.007 0.001 TYR A 176 ARG 0.002 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 133 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.864 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: 0.3968 (OUTLIER) cc_final: 0.2417 (p90) REVERT: A 48 LEU cc_start: 0.8568 (mt) cc_final: 0.8345 (mt) REVERT: A 106 VAL cc_start: 0.9252 (t) cc_final: 0.9014 (p) REVERT: A 195 ASP cc_start: 0.8192 (t70) cc_final: 0.7952 (t70) REVERT: E 222 MET cc_start: 0.6306 (mmp) cc_final: 0.6063 (mmp) outliers start: 8 outliers final: 6 residues processed: 127 average time/residue: 0.3066 time to fit residues: 53.8961 Evaluate side-chains 130 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5633 Z= 0.304 Angle : 0.539 4.817 7674 Z= 0.293 Chirality : 0.038 0.145 894 Planarity : 0.004 0.047 921 Dihedral : 3.816 17.047 752 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.92 % Allowed : 9.97 % 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: 1.31 (0.32), residues: 686 helix: 1.37 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.58 (0.50), residues: 166 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 0.013 0.001 PHE E 253 TYR 0.011 0.001 TYR A 176 ARG 0.003 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 140 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.210 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: 0.4149 (OUTLIER) cc_final: 0.2418 (p90) REVERT: A 106 VAL cc_start: 0.9301 (t) cc_final: 0.9073 (p) REVERT: A 195 ASP cc_start: 0.8455 (t70) cc_final: 0.8172 (t70) REVERT: E 222 MET cc_start: 0.6525 (mmp) cc_final: 0.6244 (mmp) outliers start: 11 outliers final: 9 residues processed: 131 average time/residue: 0.3348 time to fit residues: 58.7176 Evaluate side-chains 131 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7878 moved from start: 0.2240 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= 0.209 Angle : 0.508 5.476 7674 Z= 0.268 Chirality : 0.037 0.144 894 Planarity : 0.004 0.047 921 Dihedral : 3.759 16.476 752 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.57 % Allowed : 11.89 % 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: 1.49 (0.32), residues: 686 helix: 1.50 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.51 (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 0.011 0.001 PHE A 66 TYR 0.008 0.001 TYR A 176 ARG 0.002 0.000 ARG E 285 *********************** 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 128 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.4133 (OUTLIER) cc_final: 0.2488 (p90) REVERT: A 106 VAL cc_start: 0.9296 (t) cc_final: 0.9068 (p) REVERT: A 195 ASP cc_start: 0.8378 (t70) cc_final: 0.8072 (t70) REVERT: E 222 MET cc_start: 0.6561 (mmp) cc_final: 0.6315 (mmp) outliers start: 9 outliers final: 8 residues processed: 122 average time/residue: 0.2992 time to fit residues: 50.2103 Evaluate side-chains 126 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5633 Z= 0.212 Angle : 0.500 5.766 7674 Z= 0.265 Chirality : 0.036 0.148 894 Planarity : 0.004 0.049 921 Dihedral : 3.711 16.661 752 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.57 % Allowed : 11.71 % 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: 1.60 (0.32), residues: 686 helix: 1.59 (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 0.008 0.001 PHE A 66 TYR 0.008 0.001 TYR E 97 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 129 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.4071 (OUTLIER) cc_final: 0.2443 (p90) REVERT: A 117 TYR cc_start: 0.6448 (t80) cc_final: 0.6072 (t80) REVERT: A 195 ASP cc_start: 0.8381 (t70) cc_final: 0.8090 (t70) outliers start: 9 outliers final: 7 residues processed: 123 average time/residue: 0.3289 time to fit residues: 55.7613 Evaluate side-chains 126 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 348 MET 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: 5.9990 chunk 19 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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: 0.7865 moved from start: 0.2408 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= 0.198 Angle : 0.503 5.422 7674 Z= 0.263 Chirality : 0.036 0.156 894 Planarity : 0.004 0.050 921 Dihedral : 3.678 16.572 752 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.40 % Allowed : 12.76 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.32), residues: 686 helix: 1.64 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.54 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 132 HIS 0.004 0.001 HIS A 8 PHE 0.008 0.001 PHE A 66 TYR 0.008 0.001 TYR E 97 ARG 0.002 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 128 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.000 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: 0.4096 (OUTLIER) cc_final: 0.2491 (p90) REVERT: A 106 VAL cc_start: 0.9279 (t) cc_final: 0.9067 (p) REVERT: A 117 TYR cc_start: 0.6455 (t80) cc_final: 0.6172 (t80) REVERT: A 195 ASP cc_start: 0.8380 (t70) cc_final: 0.8092 (t70) outliers start: 8 outliers final: 5 residues processed: 123 average time/residue: 0.3061 time to fit residues: 51.4861 Evaluate side-chains 124 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain E residue 348 MET 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: 0.9990 chunk 54 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 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: 0.8980 chunk 50 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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: 0.2449 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= 0.162 Angle : 0.484 5.488 7674 Z= 0.252 Chirality : 0.036 0.151 894 Planarity : 0.004 0.050 921 Dihedral : 3.575 16.309 752 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.40 % Allowed : 12.76 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.32), residues: 686 helix: 1.81 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.42 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 132 HIS 0.003 0.001 HIS A 8 PHE 0.006 0.001 PHE A 66 TYR 0.007 0.001 TYR E 97 ARG 0.001 0.000 ARG E 360 ********************** 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 128 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.836 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: 0.4083 (OUTLIER) cc_final: 0.2544 (p90) REVERT: A 106 VAL cc_start: 0.9255 (t) cc_final: 0.9036 (p) REVERT: A 117 TYR cc_start: 0.6406 (t80) cc_final: 0.6177 (t80) REVERT: A 195 ASP cc_start: 0.8319 (t70) cc_final: 0.8097 (t70) outliers start: 8 outliers final: 7 residues processed: 123 average time/residue: 0.3051 time to fit residues: 51.4988 Evaluate side-chains 126 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain E residue 311 PHE Chi-restraints excluded: chain E residue 348 MET 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 54 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.167376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.144636 restraints weight = 17730.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.148088 restraints weight = 12456.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.150737 restraints weight = 9696.015| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5633 Z= 0.169 Angle : 0.483 4.846 7674 Z= 0.252 Chirality : 0.036 0.150 894 Planarity : 0.004 0.051 921 Dihedral : 3.540 16.579 752 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.40 % Allowed : 12.94 % Favored : 85.66 % 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: 2.00 (0.32), residues: 686 helix: 1.88 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.42 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 132 HIS 0.003 0.001 HIS A 8 PHE 0.005 0.001 PHE A 66 TYR 0.007 0.001 TYR E 97 ARG 0.001 0.000 ARG E 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2936.69 seconds wall clock time: 51 minutes 29.82 seconds (3089.82 seconds total)