Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 15:27:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/08_2023/7wd8_32434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/08_2023/7wd8_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_32434/08_2023/7wd8_32434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/08_2023/7wd8_32434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/08_2023/7wd8_32434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wd8_32434/08_2023/7wd8_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 2.83, per 1000 atoms: 0.70 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: 1.59 Conformation dependent library (CDL) restraints added in 698.5 milliseconds 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: 0.58 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: 1.21 Time building geometry restraints manager: 1.71 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: 0.010 Normalize map: mean=0, sd=1: 0.240 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: 1.000 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.950 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.200 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1989 time to fit residues: 49.7374 Evaluate side-chains 122 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6705 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN E 6 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 46 GLN F 142 ASN F 194 ASN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 4130 Z= 0.385 Angle : 0.808 7.797 5628 Z= 0.422 Chirality : 0.049 0.206 635 Planarity : 0.006 0.050 722 Dihedral : 5.992 38.453 559 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.22 % 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: -0.42 (0.35), residues: 516 helix: -1.58 (1.65), residues: 12 sheet: 0.28 (0.34), residues: 214 loop : -0.62 (0.34), residues: 290 *********************** 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 135 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1414 time to fit residues: 23.2090 Evaluate side-chains 103 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6749 ------------------------------------------------------------------------------- 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: 2.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 160 GLN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4130 Z= 0.226 Angle : 0.638 7.894 5628 Z= 0.327 Chirality : 0.045 0.189 635 Planarity : 0.005 0.045 722 Dihedral : 5.249 27.800 559 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.00 % 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: -0.09 (0.36), residues: 516 helix: -1.44 (1.58), residues: 12 sheet: 0.67 (0.36), residues: 208 loop : -0.51 (0.34), residues: 296 *********************** 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 134 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1922 time to fit residues: 30.8493 Evaluate side-chains 102 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6806 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.6679 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= 0.248 Angle : 0.641 7.342 5628 Z= 0.332 Chirality : 0.046 0.185 635 Planarity : 0.005 0.050 722 Dihedral : 5.231 24.840 559 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.00 % 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: -0.08 (0.36), residues: 516 helix: -0.93 (1.63), residues: 12 sheet: 0.77 (0.36), residues: 208 loop : -0.61 (0.35), residues: 296 *********************** 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 133 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1584 time to fit residues: 25.5389 Evaluate side-chains 101 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6405 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 44 optimal weight: 0.0000 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4130 Z= 0.165 Angle : 0.583 6.865 5628 Z= 0.298 Chirality : 0.044 0.172 635 Planarity : 0.005 0.052 722 Dihedral : 4.911 26.215 559 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.00 % 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: -0.08 (0.37), residues: 516 helix: -0.62 (1.33), residues: 18 sheet: 0.86 (0.37), residues: 195 loop : -0.64 (0.35), residues: 303 *********************** 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 136 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1833 time to fit residues: 30.0771 Evaluate side-chains 99 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6451 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN ** 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: 0.6707 moved from start: 0.7395 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= 0.251 Angle : 0.659 7.103 5628 Z= 0.338 Chirality : 0.045 0.174 635 Planarity : 0.005 0.052 722 Dihedral : 5.296 25.545 559 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.07 % Favored : 95.74 % Rotamer Outliers : 0.00 % 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: -0.23 (0.36), residues: 516 helix: -0.74 (1.85), residues: 12 sheet: 0.57 (0.36), residues: 193 loop : -0.60 (0.35), residues: 311 *********************** 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 128 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1856 time to fit residues: 28.7676 Evaluate side-chains 105 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6539 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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 ** 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: 0.6663 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4130 Z= 0.177 Angle : 0.608 7.019 5628 Z= 0.311 Chirality : 0.044 0.166 635 Planarity : 0.005 0.054 722 Dihedral : 5.008 25.871 559 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.68 % Favored : 96.12 % Rotamer Outliers : 0.00 % 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: -0.32 (0.36), residues: 516 helix: -0.69 (1.82), residues: 12 sheet: 0.54 (0.36), residues: 195 loop : -0.69 (0.34), residues: 309 *********************** 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 131 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1722 time to fit residues: 27.4856 Evaluate side-chains 107 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6360 ------------------------------------------------------------------------------- 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: 8.9990 chunk 4 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 14 optimal weight: 6.9990 overall best weight: 2.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 4130 Z= 0.278 Angle : 0.691 7.690 5628 Z= 0.357 Chirality : 0.046 0.189 635 Planarity : 0.005 0.052 722 Dihedral : 5.614 25.692 559 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.81 % Favored : 93.99 % Rotamer Outliers : 0.00 % 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: -0.53 (0.36), residues: 516 helix: None (None), residues: 0 sheet: 0.25 (0.35), residues: 205 loop : -0.76 (0.34), residues: 311 *********************** 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 126 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1546 time to fit residues: 24.1592 Evaluate side-chains 99 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5794 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.8239 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= 0.254 Angle : 0.680 8.696 5628 Z= 0.348 Chirality : 0.046 0.168 635 Planarity : 0.005 0.056 722 Dihedral : 5.655 25.994 559 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.84 % Favored : 94.96 % Rotamer Outliers : 0.00 % 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: -0.54 (0.36), residues: 516 helix: None (None), residues: 0 sheet: 0.27 (0.36), residues: 201 loop : -0.78 (0.35), residues: 315 *********************** 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 121 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1596 time to fit residues: 23.9082 Evaluate side-chains 106 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6492 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.8274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4130 Z= 0.191 Angle : 0.636 8.040 5628 Z= 0.327 Chirality : 0.046 0.162 635 Planarity : 0.005 0.061 722 Dihedral : 5.362 26.017 559 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.46 % Favored : 95.35 % Rotamer Outliers : 0.00 % 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: -0.51 (0.37), residues: 516 helix: None (None), residues: 0 sheet: 0.20 (0.36), residues: 207 loop : -0.71 (0.35), residues: 309 ********************** 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 119 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1587 time to fit residues: 23.4107 Evaluate side-chains 101 residues out of total 457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5934 ------------------------------------------------------------------------------- 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: 5.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.140093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117050 restraints weight = 8773.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120724 restraints weight = 5448.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123371 restraints weight = 3776.697| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.8586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 4130 Z= 0.322 Angle : 0.737 10.007 5628 Z= 0.380 Chirality : 0.047 0.173 635 Planarity : 0.006 0.059 722 Dihedral : 5.950 26.890 559 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.17 % Favored : 92.64 % Rotamer Outliers : 0.00 % 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: -0.68 (0.37), residues: 516 helix: None (None), residues: 0 sheet: 0.08 (0.34), residues: 211 loop : -0.83 (0.36), residues: 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1256.90 seconds wall clock time: 25 minutes 7.30 seconds (1507.30 seconds total)