Starting phenix.real_space_refine on Sun Mar 10 18:38:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/03_2024/7wd8_32434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/03_2024/7wd8_32434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/03_2024/7wd8_32434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/03_2024/7wd8_32434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/03_2024/7wd8_32434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/03_2024/7wd8_32434.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2540 2.51 5 N 678 2.21 5 O 793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4029 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 163 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 3, 'TRANS': 16} Chain: "E" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 548 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Time building chain proxies: 2.72, per 1000 atoms: 0.68 Number of scatterers: 4029 At special positions: 0 Unit cell: (95.091, 96.184, 64.487, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 793 8.00 N 678 7.00 C 2540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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: 1.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 12 sheets defined 5.5% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 83 through 87 removed outlier: 4.004A pdb=" N ALA F 87 " --> pdb=" O GLU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 131 removed outlier: 3.997A pdb=" N SER F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 3.509A pdb=" N GLU F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG F 192 " --> pdb=" O ASP F 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 187 through 192' Processing helix chain 'B' and resid 525 through 530 removed outlier: 4.061A pdb=" N LYS B 529 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 530 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.749A pdb=" N ILE A 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 566 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.611A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.687A pdb=" N THR E 117 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 114 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET E 34 " --> pdb=" O MET E 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 57 " --> pdb=" O HIS E 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.687A pdb=" N THR E 117 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 114 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP E 106 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 127 through 131 removed outlier: 6.585A pdb=" N TYR E 182 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 127 through 131 removed outlier: 6.585A pdb=" N TYR E 182 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.532A pdb=" N LYS E 215 " --> pdb=" O CYS E 202 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 211 " --> pdb=" O HIS E 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.759A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP F 74 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER F 71 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.866A pdb=" N TRP F 39 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER F 57 " --> pdb=" O TYR F 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 14 removed outlier: 4.016A pdb=" N HIS F 94 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA F 101 " --> pdb=" O HIS F 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 118 through 122 removed outlier: 3.752A pdb=" N VAL F 137 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR F 177 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER F 180 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER F 166 " --> pdb=" O SER F 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 149 through 154 removed outlier: 3.665A pdb=" N TYR F 196 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE F 213 " --> pdb=" O TYR F 196 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA F 200 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE F 209 " --> pdb=" O ALA F 200 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1291 1.35 - 1.46: 1003 1.46 - 1.58: 1812 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 4130 Sorted by residual: bond pdb=" N GLN B 580 " pdb=" CA GLN B 580 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.85e-01 bond pdb=" CA VAL E 190 " pdb=" CB VAL E 190 " ideal model delta sigma weight residual 1.546 1.538 0.009 8.80e-03 1.29e+04 9.41e-01 bond pdb=" C PHE E 153 " pdb=" O PHE E 153 " ideal model delta sigma weight residual 1.240 1.230 0.010 1.29e-02 6.01e+03 6.53e-01 bond pdb=" C SER F 7 " pdb=" O SER F 7 " ideal model delta sigma weight residual 1.240 1.230 0.010 1.29e-02 6.01e+03 6.25e-01 bond pdb=" CB PRO F 145 " pdb=" CG PRO F 145 " ideal model delta sigma weight residual 1.506 1.477 0.029 3.90e-02 6.57e+02 5.71e-01 ... (remaining 4125 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.30: 189 107.30 - 113.98: 2322 113.98 - 120.65: 1477 120.65 - 127.33: 1590 127.33 - 134.00: 50 Bond angle restraints: 5628 Sorted by residual: angle pdb=" C LYS E 65 " pdb=" N ASP E 66 " pdb=" CA ASP E 66 " ideal model delta sigma weight residual 121.54 126.28 -4.74 1.91e+00 2.74e-01 6.15e+00 angle pdb=" N GLY B 526 " pdb=" CA GLY B 526 " pdb=" C GLY B 526 " ideal model delta sigma weight residual 112.34 116.05 -3.71 2.04e+00 2.40e-01 3.30e+00 angle pdb=" C TYR F 144 " pdb=" N PRO F 145 " pdb=" CA PRO F 145 " ideal model delta sigma weight residual 127.00 131.31 -4.31 2.40e+00 1.74e-01 3.22e+00 angle pdb=" NE ARG F 65 " pdb=" CZ ARG F 65 " pdb=" NH1 ARG F 65 " ideal model delta sigma weight residual 121.50 119.88 1.62 1.00e+00 1.00e+00 2.64e+00 angle pdb=" CA LEU E 184 " pdb=" CB LEU E 184 " pdb=" CG LEU E 184 " ideal model delta sigma weight residual 116.30 121.81 -5.51 3.50e+00 8.16e-02 2.48e+00 ... (remaining 5623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 2394 11.72 - 23.45: 69 23.45 - 35.17: 19 35.17 - 46.89: 3 46.89 - 58.61: 1 Dihedral angle restraints: 2486 sinusoidal: 962 harmonic: 1524 Sorted by residual: dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N ASP E 102 " pdb=" CA ASP E 102 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PRO B 527 " pdb=" C PRO B 527 " pdb=" N LYS B 528 " pdb=" CA LYS B 528 " ideal model delta harmonic sigma weight residual 180.00 -164.83 -15.17 0 5.00e+00 4.00e-02 9.20e+00 dihedral pdb=" CA CYS B 525 " pdb=" C CYS B 525 " pdb=" N GLY B 526 " pdb=" CA GLY B 526 " ideal model delta harmonic sigma weight residual 180.00 166.45 13.55 0 5.00e+00 4.00e-02 7.34e+00 ... (remaining 2483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 407 0.029 - 0.058: 145 0.058 - 0.087: 26 0.087 - 0.116: 52 0.116 - 0.145: 5 Chirality restraints: 635 Sorted by residual: chirality pdb=" CA ILE F 148 " pdb=" N ILE F 148 " pdb=" C ILE F 148 " pdb=" CB ILE F 148 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE B 584 " pdb=" N ILE B 584 " pdb=" C ILE B 584 " pdb=" CB ILE B 584 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA HIS F 80 " pdb=" N HIS F 80 " pdb=" C HIS F 80 " pdb=" CB HIS F 80 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 632 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 579 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 173 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO E 174 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E 195 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO E 196 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.019 5.00e-02 4.00e+02 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 641 2.78 - 3.31: 3473 3.31 - 3.84: 6321 3.84 - 4.37: 6980 4.37 - 4.90: 12506 Nonbonded interactions: 29921 Sorted by model distance: nonbonded pdb=" O VAL A 327 " pdb=" OG1 THR B 531 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN E 140 " pdb=" N SER E 141 " model vdw 2.303 2.520 nonbonded pdb=" OD1 ASN A 334 " pdb=" N LEU A 335 " model vdw 2.306 2.520 nonbonded pdb=" OD2 ASP F 174 " pdb=" OG1 THR F 176 " model vdw 2.317 2.440 nonbonded pdb=" OD2 ASP E 55 " pdb=" NZ LYS B 537 " model vdw 2.334 2.520 ... (remaining 29916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 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: 0.830 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 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 : 0.002 0.029 4130 Z= 0.119 Angle : 0.507 7.502 5628 Z= 0.280 Chirality : 0.041 0.145 635 Planarity : 0.005 0.042 722 Dihedral : 6.426 58.615 1487 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.07 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.96 (0.31), residues: 516 helix: -3.53 (0.66), residues: 18 sheet: -0.06 (0.30), residues: 219 loop : -0.86 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 110 HIS 0.007 0.001 HIS F 80 PHE 0.006 0.001 PHE F 102 TYR 0.011 0.001 TYR E 103 ARG 0.003 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 VAL cc_start: 0.4988 (t) cc_final: 0.4697 (t) REVERT: E 5 GLN cc_start: 0.6832 (mt0) cc_final: 0.6417 (tm-30) REVERT: E 6 GLN cc_start: 0.7567 (mt0) cc_final: 0.7314 (mt0) REVERT: E 65 LYS cc_start: 0.5878 (tttm) cc_final: 0.5573 (ttpp) REVERT: E 82 GLN cc_start: 0.7258 (tt0) cc_final: 0.6232 (mp10) REVERT: E 148 LEU cc_start: 0.7730 (tp) cc_final: 0.7499 (tp) REVERT: E 178 GLN cc_start: 0.7258 (tt0) cc_final: 0.6581 (pm20) REVERT: E 180 ASP cc_start: 0.6898 (m-30) cc_final: 0.6681 (m-30) REVERT: E 189 THR cc_start: 0.6413 (m) cc_final: 0.6169 (p) REVERT: F 86 ASP cc_start: 0.7319 (m-30) cc_final: 0.6747 (m-30) REVERT: B 535 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7924 (ttmt) REVERT: B 559 PHE cc_start: 0.6026 (m-10) cc_final: 0.5416 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1987 time to fit residues: 49.3749 Evaluate side-chains 125 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN E 203 ASN F 41 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN F 194 ASN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4130 Z= 0.239 Angle : 0.639 6.177 5628 Z= 0.331 Chirality : 0.044 0.145 635 Planarity : 0.005 0.035 722 Dihedral : 4.807 30.285 559 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.18 (0.34), residues: 516 helix: -2.04 (1.59), residues: 12 sheet: 0.45 (0.32), residues: 225 loop : -0.46 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 110 HIS 0.003 0.001 HIS F 94 PHE 0.018 0.002 PHE F 75 TYR 0.010 0.002 TYR E 109 ARG 0.006 0.001 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.6903 (mt0) cc_final: 0.6069 (tm-30) REVERT: E 6 GLN cc_start: 0.7693 (mt0) cc_final: 0.7477 (mt0) REVERT: E 65 LYS cc_start: 0.5957 (tttm) cc_final: 0.5561 (ttpp) REVERT: F 79 ILE cc_start: 0.7786 (mm) cc_final: 0.7514 (mm) REVERT: F 92 CYS cc_start: 0.3775 (p) cc_final: 0.3364 (p) REVERT: B 552 LEU cc_start: 0.8890 (mm) cc_final: 0.8657 (mm) REVERT: B 559 PHE cc_start: 0.6435 (m-10) cc_final: 0.5943 (m-80) REVERT: B 587 ILE cc_start: 0.7047 (mm) cc_final: 0.6830 (mp) REVERT: B 588 THR cc_start: 0.8085 (m) cc_final: 0.7601 (p) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1689 time to fit residues: 28.9287 Evaluate side-chains 109 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 ASN F 142 ASN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4130 Z= 0.174 Angle : 0.580 7.415 5628 Z= 0.294 Chirality : 0.044 0.158 635 Planarity : 0.004 0.036 722 Dihedral : 4.571 27.522 559 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 0.12 (0.36), residues: 516 helix: -1.69 (1.19), residues: 18 sheet: 0.82 (0.34), residues: 225 loop : -0.39 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 110 HIS 0.003 0.001 HIS F 94 PHE 0.008 0.001 PHE E 153 TYR 0.015 0.001 TYR F 53 ARG 0.004 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.6964 (mt0) cc_final: 0.6211 (tm-30) REVERT: E 63 LYS cc_start: 0.7837 (tttt) cc_final: 0.7243 (tppt) REVERT: F 77 LEU cc_start: 0.8243 (tp) cc_final: 0.7872 (tp) REVERT: F 79 ILE cc_start: 0.7883 (mm) cc_final: 0.7452 (mm) REVERT: F 83 GLU cc_start: 0.5559 (mp0) cc_final: 0.5034 (mm-30) REVERT: B 559 PHE cc_start: 0.6497 (m-10) cc_final: 0.6238 (m-80) REVERT: B 588 THR cc_start: 0.7902 (m) cc_final: 0.7426 (p) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1796 time to fit residues: 30.5611 Evaluate side-chains 108 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 203 ASN F 160 GLN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4130 Z= 0.146 Angle : 0.543 6.448 5628 Z= 0.277 Chirality : 0.043 0.154 635 Planarity : 0.004 0.050 722 Dihedral : 4.408 28.107 559 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: 0.35 (0.37), residues: 516 helix: -1.47 (1.17), residues: 18 sheet: 1.06 (0.34), residues: 232 loop : -0.37 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 36 HIS 0.002 0.001 HIS F 94 PHE 0.016 0.001 PHE E 153 TYR 0.013 0.001 TYR E 109 ARG 0.004 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7242 (mt0) cc_final: 0.6285 (tm-30) REVERT: E 63 LYS cc_start: 0.7748 (tttt) cc_final: 0.7243 (tppt) REVERT: F 4 LEU cc_start: 0.8644 (mt) cc_final: 0.8433 (mt) REVERT: F 77 LEU cc_start: 0.8238 (tp) cc_final: 0.7870 (tp) REVERT: F 79 ILE cc_start: 0.7948 (mm) cc_final: 0.7569 (mm) REVERT: F 92 CYS cc_start: 0.3649 (p) cc_final: 0.3075 (p) REVERT: F 96 ARG cc_start: 0.7977 (tpt90) cc_final: 0.7776 (tpt90) REVERT: F 179 MET cc_start: 0.7334 (tmm) cc_final: 0.6772 (tmm) REVERT: B 530 SER cc_start: 0.8026 (p) cc_final: 0.7796 (m) REVERT: B 559 PHE cc_start: 0.6346 (m-10) cc_final: 0.5804 (m-80) REVERT: B 577 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7367 (mtm110) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1770 time to fit residues: 29.8453 Evaluate side-chains 108 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 0.4980 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN E 112 GLN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.7152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 4130 Z= 0.460 Angle : 0.872 12.321 5628 Z= 0.449 Chirality : 0.050 0.227 635 Planarity : 0.006 0.038 722 Dihedral : 6.331 20.568 559 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.22 % Allowed : 3.06 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.17 (0.37), residues: 516 helix: -1.54 (2.87), residues: 6 sheet: 0.53 (0.36), residues: 212 loop : -0.53 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 110 HIS 0.009 0.002 HIS F 94 PHE 0.025 0.003 PHE E 173 TYR 0.033 0.003 TYR E 101 ARG 0.005 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7402 (mt0) cc_final: 0.6311 (tm-30) REVERT: E 50 MET cc_start: 0.7805 (ttp) cc_final: 0.7593 (ttp) REVERT: E 55 ASP cc_start: 0.8495 (p0) cc_final: 0.8009 (p0) REVERT: E 57 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6755 (mm-30) REVERT: E 63 LYS cc_start: 0.8129 (tttt) cc_final: 0.7715 (tppt) REVERT: F 96 ARG cc_start: 0.8263 (tpt90) cc_final: 0.7903 (tpt90) REVERT: F 197 THR cc_start: 0.5411 (m) cc_final: 0.5062 (m) REVERT: F 199 GLU cc_start: 0.4878 (tm-30) cc_final: 0.3430 (mp0) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2048 time to fit residues: 32.9495 Evaluate side-chains 106 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 46 GLN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4130 Z= 0.163 Angle : 0.630 9.280 5628 Z= 0.314 Chirality : 0.044 0.163 635 Planarity : 0.005 0.044 722 Dihedral : 5.089 24.076 559 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.20 (0.37), residues: 516 helix: -0.57 (1.42), residues: 18 sheet: 0.64 (0.35), residues: 216 loop : -0.71 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 161 HIS 0.002 0.001 HIS F 94 PHE 0.010 0.001 PHE E 173 TYR 0.023 0.002 TYR F 177 ARG 0.009 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7382 (mt0) cc_final: 0.6355 (tm-30) REVERT: E 57 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6557 (mm-30) REVERT: E 63 LYS cc_start: 0.7934 (tttt) cc_final: 0.7415 (tppt) REVERT: E 107 PHE cc_start: 0.8091 (m-10) cc_final: 0.7786 (m-80) REVERT: E 195 TRP cc_start: 0.6852 (t60) cc_final: 0.5810 (t60) REVERT: F 4 LEU cc_start: 0.8574 (mt) cc_final: 0.8117 (tp) REVERT: F 79 ILE cc_start: 0.7907 (mm) cc_final: 0.7416 (mm) REVERT: F 92 CYS cc_start: 0.2965 (p) cc_final: 0.1923 (p) REVERT: F 96 ARG cc_start: 0.8162 (tpt90) cc_final: 0.7960 (tpt90) REVERT: F 109 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6737 (tm-30) REVERT: F 171 ASP cc_start: 0.7536 (m-30) cc_final: 0.7304 (m-30) REVERT: F 179 MET cc_start: 0.7612 (tmm) cc_final: 0.7209 (tmm) REVERT: F 199 GLU cc_start: 0.4645 (tm-30) cc_final: 0.3543 (mp0) REVERT: B 577 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7236 (mtm180) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1874 time to fit residues: 30.4653 Evaluate side-chains 111 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4130 Z= 0.253 Angle : 0.674 9.581 5628 Z= 0.341 Chirality : 0.045 0.153 635 Planarity : 0.005 0.041 722 Dihedral : 5.289 22.645 559 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.23 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.32 (0.36), residues: 516 helix: -1.53 (3.02), residues: 6 sheet: 0.41 (0.35), residues: 212 loop : -0.62 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 110 HIS 0.004 0.001 HIS F 94 PHE 0.013 0.002 PHE E 173 TYR 0.021 0.002 TYR F 177 ARG 0.006 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.4800 (m-10) cc_final: 0.4511 (m-80) REVERT: E 5 GLN cc_start: 0.7414 (mt0) cc_final: 0.6394 (tm-30) REVERT: E 57 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6697 (mm-30) REVERT: E 63 LYS cc_start: 0.8022 (tttt) cc_final: 0.7518 (tppt) REVERT: E 117 THR cc_start: 0.6408 (m) cc_final: 0.6204 (m) REVERT: E 152 TYR cc_start: 0.6388 (p90) cc_final: 0.6177 (p90) REVERT: F 4 LEU cc_start: 0.8447 (mt) cc_final: 0.8060 (mt) REVERT: F 92 CYS cc_start: 0.3074 (p) cc_final: 0.2790 (p) REVERT: F 96 ARG cc_start: 0.8137 (tpt90) cc_final: 0.7771 (tpt90) REVERT: F 179 MET cc_start: 0.7601 (tmm) cc_final: 0.7293 (tmm) REVERT: F 199 GLU cc_start: 0.4567 (tm-30) cc_final: 0.3584 (mp0) REVERT: B 535 LYS cc_start: 0.8273 (tppt) cc_final: 0.8021 (tptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1734 time to fit residues: 26.4870 Evaluate side-chains 101 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN E 35 ASN F 46 GLN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4130 Z= 0.230 Angle : 0.659 8.812 5628 Z= 0.335 Chirality : 0.045 0.158 635 Planarity : 0.005 0.055 722 Dihedral : 5.239 23.201 559 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.07 % Favored : 95.74 % Rotamer: Outliers : 0.22 % Allowed : 1.09 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.35 (0.36), residues: 516 helix: -1.83 (2.95), residues: 6 sheet: 0.35 (0.34), residues: 214 loop : -0.62 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 110 HIS 0.004 0.001 HIS F 38 PHE 0.012 0.002 PHE E 173 TYR 0.024 0.002 TYR F 177 ARG 0.006 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7369 (mt0) cc_final: 0.6307 (tm-30) REVERT: E 57 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6691 (mm-30) REVERT: E 63 LYS cc_start: 0.7998 (tttt) cc_final: 0.7545 (tppt) REVERT: E 152 TYR cc_start: 0.6469 (p90) cc_final: 0.6243 (p90) REVERT: F 79 ILE cc_start: 0.7730 (mm) cc_final: 0.7463 (mm) REVERT: F 92 CYS cc_start: 0.2976 (p) cc_final: 0.2692 (p) REVERT: F 96 ARG cc_start: 0.8171 (tpt90) cc_final: 0.7729 (tpt90) REVERT: F 97 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6735 (mt-10) REVERT: F 109 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6820 (tm-30) REVERT: F 147 ASP cc_start: 0.7370 (p0) cc_final: 0.6881 (p0) REVERT: F 179 MET cc_start: 0.7753 (tmm) cc_final: 0.7518 (tmm) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.1658 time to fit residues: 24.6906 Evaluate side-chains 99 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 45 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4130 Z= 0.188 Angle : 0.618 7.618 5628 Z= 0.313 Chirality : 0.044 0.151 635 Planarity : 0.005 0.048 722 Dihedral : 5.033 24.373 559 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.88 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.52 (0.36), residues: 516 helix: -0.64 (1.43), residues: 18 sheet: 0.21 (0.35), residues: 202 loop : -0.69 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 110 HIS 0.003 0.001 HIS F 38 PHE 0.010 0.002 PHE E 173 TYR 0.017 0.002 TYR F 177 ARG 0.005 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7391 (mt0) cc_final: 0.6273 (tm-30) REVERT: E 57 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6863 (mm-30) REVERT: E 63 LYS cc_start: 0.8024 (tttt) cc_final: 0.7476 (tppt) REVERT: E 112 GLN cc_start: 0.7699 (tp40) cc_final: 0.7455 (tp40) REVERT: F 79 ILE cc_start: 0.7610 (mm) cc_final: 0.7331 (mm) REVERT: F 96 ARG cc_start: 0.8239 (tpt90) cc_final: 0.7777 (tpt90) REVERT: F 97 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6768 (mt-10) REVERT: F 109 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6773 (tm-30) REVERT: F 147 ASP cc_start: 0.7413 (p0) cc_final: 0.7096 (p0) REVERT: F 179 MET cc_start: 0.7766 (tmm) cc_final: 0.7485 (tmm) REVERT: B 559 PHE cc_start: 0.6520 (m-80) cc_final: 0.6154 (m-80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1630 time to fit residues: 24.5878 Evaluate side-chains 98 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.7938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4130 Z= 0.232 Angle : 0.660 8.543 5628 Z= 0.334 Chirality : 0.045 0.143 635 Planarity : 0.005 0.048 722 Dihedral : 5.295 24.183 559 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.84 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.46 (0.36), residues: 516 helix: -0.97 (1.79), residues: 12 sheet: 0.30 (0.36), residues: 196 loop : -0.67 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 161 HIS 0.004 0.001 HIS F 94 PHE 0.011 0.002 PHE E 173 TYR 0.019 0.002 TYR E 101 ARG 0.006 0.001 ARG F 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.4637 (m-10) cc_final: 0.4371 (m-80) REVERT: E 5 GLN cc_start: 0.7338 (mt0) cc_final: 0.6280 (tm-30) REVERT: E 63 LYS cc_start: 0.8052 (tttt) cc_final: 0.7500 (tppt) REVERT: F 79 ILE cc_start: 0.7606 (mm) cc_final: 0.7351 (mm) REVERT: F 83 GLU cc_start: 0.4728 (mp0) cc_final: 0.4259 (mm-30) REVERT: F 96 ARG cc_start: 0.8216 (tpt90) cc_final: 0.7791 (tpt90) REVERT: F 97 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6811 (mt-10) REVERT: F 109 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6773 (tm-30) REVERT: F 147 ASP cc_start: 0.7585 (p0) cc_final: 0.7375 (p0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1497 time to fit residues: 22.7005 Evaluate side-chains 102 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 34 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121739 restraints weight = 8643.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125749 restraints weight = 5355.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.128468 restraints weight = 3667.896| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4130 Z= 0.175 Angle : 0.620 7.536 5628 Z= 0.312 Chirality : 0.044 0.153 635 Planarity : 0.005 0.042 722 Dihedral : 5.083 23.931 559 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.10 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % 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: -0.50 (0.36), residues: 516 helix: -0.92 (1.38), residues: 18 sheet: 0.30 (0.34), residues: 206 loop : -0.74 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 161 HIS 0.003 0.001 HIS F 38 PHE 0.008 0.001 PHE E 173 TYR 0.013 0.002 TYR F 177 ARG 0.005 0.001 ARG B 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.30 seconds wall clock time: 24 minutes 4.07 seconds (1444.07 seconds total)