Starting phenix.real_space_refine on Fri Aug 22 14:15:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wd8_32434/08_2025/7wd8_32434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wd8_32434/08_2025/7wd8_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wd8_32434/08_2025/7wd8_32434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wd8_32434/08_2025/7wd8_32434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wd8_32434/08_2025/7wd8_32434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wd8_32434/08_2025/7wd8_32434.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.17, per 1000 atoms: 0.29 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 170.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.19 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: 0.64 Time building geometry restraints manager: 0.46 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: 0.00 - 1.50: 5514 1.50 - 3.00: 100 3.00 - 4.50: 11 4.50 - 6.00: 2 6.00 - 7.50: 1 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 3.040 nonbonded pdb=" OD1 ASN E 140 " pdb=" N SER E 141 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASN A 334 " pdb=" N LEU A 335 " model vdw 2.306 3.120 nonbonded pdb=" OD2 ASP F 174 " pdb=" OG1 THR F 176 " model vdw 2.317 3.040 nonbonded pdb=" OD2 ASP E 55 " pdb=" NZ LYS B 537 " model vdw 2.334 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.270 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: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 6.040 Find NCS groups from input model: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.770 ------------------------------------------------------------------------------- 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 4135 Z= 0.100 Angle : 0.507 7.502 5638 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 : 8.68 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG F 65 TYR 0.011 0.001 TYR E 103 PHE 0.006 0.001 PHE F 102 TRP 0.012 0.001 TRP E 110 HIS 0.007 0.001 HIS F 80 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 4130) covalent geometry : angle 0.50666 ( 5628) SS BOND : bond 0.00219 ( 5) SS BOND : angle 0.56789 ( 10) hydrogen bonds : bond 0.27312 ( 126) hydrogen bonds : angle 10.80264 ( 381) *********************** 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 to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.152 Fit side-chains 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: 0.4696 (t) REVERT: E 5 GLN cc_start: 0.6832 (mt0) cc_final: 0.6410 (tm-30) REVERT: E 6 GLN cc_start: 0.7567 (mt0) cc_final: 0.7307 (mt0) REVERT: E 65 LYS cc_start: 0.5878 (tttm) cc_final: 0.5578 (ttpp) REVERT: E 82 GLN cc_start: 0.7258 (tt0) cc_final: 0.6237 (mp10) REVERT: E 148 LEU cc_start: 0.7730 (tp) cc_final: 0.7475 (tp) REVERT: E 178 GLN cc_start: 0.7258 (tt0) cc_final: 0.6592 (pm20) REVERT: E 180 ASP cc_start: 0.6898 (m-30) cc_final: 0.6665 (m-30) REVERT: E 189 THR cc_start: 0.6413 (m) cc_final: 0.6189 (p) REVERT: F 86 ASP cc_start: 0.7319 (m-30) cc_final: 0.6616 (m-30) REVERT: B 535 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7928 (ttmt) REVERT: B 559 PHE cc_start: 0.6026 (m-10) cc_final: 0.5413 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.0894 time to fit residues: 22.4065 Evaluate side-chains 122 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN E 43 GLN E 203 ASN F 194 ASN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.154744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129678 restraints weight = 8546.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134160 restraints weight = 5235.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.137356 restraints weight = 3583.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139626 restraints weight = 2628.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.141180 restraints weight = 2042.859| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4135 Z= 0.147 Angle : 0.625 7.142 5638 Z= 0.323 Chirality : 0.045 0.157 635 Planarity : 0.005 0.033 722 Dihedral : 4.645 30.271 559 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.52 % Favored : 97.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.34), residues: 516 helix: -3.95 (0.84), residues: 6 sheet: 0.54 (0.32), residues: 225 loop : -0.57 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 18 TYR 0.009 0.001 TYR E 103 PHE 0.017 0.002 PHE F 75 TRP 0.014 0.002 TRP E 110 HIS 0.003 0.001 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4130) covalent geometry : angle 0.62160 ( 5628) SS BOND : bond 0.00988 ( 5) SS BOND : angle 1.62091 ( 10) hydrogen bonds : bond 0.03776 ( 126) hydrogen bonds : angle 6.89349 ( 381) *********************** 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 146 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7296 (mt0) cc_final: 0.6086 (tm-30) REVERT: E 65 LYS cc_start: 0.6549 (tttm) cc_final: 0.6038 (ttpp) REVERT: E 82 GLN cc_start: 0.8219 (tt0) cc_final: 0.6828 (mp10) REVERT: E 180 ASP cc_start: 0.7259 (m-30) cc_final: 0.6992 (m-30) REVERT: F 79 ILE cc_start: 0.8228 (mm) cc_final: 0.7897 (mm) REVERT: F 92 CYS cc_start: 0.3857 (p) cc_final: 0.3362 (p) REVERT: F 96 ARG cc_start: 0.8245 (tpt90) cc_final: 0.7945 (tpt90) REVERT: F 199 GLU cc_start: 0.5026 (tm-30) cc_final: 0.4620 (mt-10) REVERT: B 535 LYS cc_start: 0.8534 (ttmt) cc_final: 0.7908 (tttt) REVERT: B 552 LEU cc_start: 0.9065 (mm) cc_final: 0.8824 (mm) REVERT: B 559 PHE cc_start: 0.6474 (m-10) cc_final: 0.5891 (m-80) REVERT: B 583 GLU cc_start: 0.7361 (pm20) cc_final: 0.7132 (pm20) REVERT: B 587 ILE cc_start: 0.7138 (mm) cc_final: 0.6870 (mp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0649 time to fit residues: 11.4662 Evaluate side-chains 115 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 203 ASN F 41 GLN F 46 GLN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121197 restraints weight = 8653.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125550 restraints weight = 5268.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128542 restraints weight = 3583.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.130777 restraints weight = 2637.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132260 restraints weight = 2039.458| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4135 Z= 0.222 Angle : 0.731 7.521 5638 Z= 0.374 Chirality : 0.047 0.152 635 Planarity : 0.005 0.050 722 Dihedral : 5.476 29.035 559 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.36), residues: 516 helix: -1.85 (1.53), residues: 12 sheet: 0.78 (0.35), residues: 219 loop : -0.45 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 112 TYR 0.019 0.002 TYR F 190 PHE 0.010 0.002 PHE E 173 TRP 0.021 0.003 TRP E 110 HIS 0.005 0.002 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 4130) covalent geometry : angle 0.72681 ( 5628) SS BOND : bond 0.00870 ( 5) SS BOND : angle 1.95773 ( 10) hydrogen bonds : bond 0.03935 ( 126) hydrogen bonds : angle 6.73350 ( 381) *********************** 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 140 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7215 (mt0) cc_final: 0.6099 (tm-30) REVERT: E 57 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6654 (mm-30) REVERT: F 4 LEU cc_start: 0.8685 (mt) cc_final: 0.8369 (mt) REVERT: F 37 MET cc_start: 0.7447 (mmm) cc_final: 0.7207 (tpp) REVERT: F 78 ASN cc_start: 0.7996 (m-40) cc_final: 0.7691 (m-40) REVERT: F 79 ILE cc_start: 0.8432 (mm) cc_final: 0.7886 (mm) REVERT: F 92 CYS cc_start: 0.3085 (p) cc_final: 0.2818 (p) REVERT: F 96 ARG cc_start: 0.8490 (tpt90) cc_final: 0.7949 (tpt90) REVERT: F 179 MET cc_start: 0.7473 (tmm) cc_final: 0.6973 (tmm) REVERT: F 215 ARG cc_start: 0.6722 (tpm170) cc_final: 0.6394 (tpp80) REVERT: B 535 LYS cc_start: 0.8469 (ttmt) cc_final: 0.7649 (ttmt) REVERT: B 552 LEU cc_start: 0.8832 (mm) cc_final: 0.8512 (mm) REVERT: B 559 PHE cc_start: 0.6642 (m-10) cc_final: 0.5993 (m-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0719 time to fit residues: 12.2619 Evaluate side-chains 107 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- 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 ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117710 restraints weight = 8850.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121674 restraints weight = 5472.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.124511 restraints weight = 3772.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126513 restraints weight = 2793.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127861 restraints weight = 2195.151| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4135 Z= 0.234 Angle : 0.731 8.017 5638 Z= 0.379 Chirality : 0.046 0.153 635 Planarity : 0.005 0.044 722 Dihedral : 5.782 26.035 559 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.36), residues: 516 helix: -1.65 (1.54), residues: 12 sheet: 0.89 (0.36), residues: 211 loop : -0.75 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 577 TYR 0.028 0.003 TYR F 177 PHE 0.014 0.002 PHE E 173 TRP 0.026 0.003 TRP E 110 HIS 0.005 0.001 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 4130) covalent geometry : angle 0.72548 ( 5628) SS BOND : bond 0.00978 ( 5) SS BOND : angle 2.16553 ( 10) hydrogen bonds : bond 0.03946 ( 126) hydrogen bonds : angle 6.76358 ( 381) *********************** 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 130 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7540 (mt0) cc_final: 0.6299 (tm-30) REVERT: E 57 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6497 (mm-30) REVERT: E 99 LYS cc_start: 0.7889 (tttt) cc_final: 0.7662 (tttt) REVERT: E 112 GLN cc_start: 0.7851 (tp40) cc_final: 0.7553 (tp-100) REVERT: F 96 ARG cc_start: 0.8455 (tpt90) cc_final: 0.7995 (tpt90) REVERT: F 190 TYR cc_start: 0.6693 (t80) cc_final: 0.6442 (t80) REVERT: F 197 THR cc_start: 0.5017 (m) cc_final: 0.4624 (m) REVERT: F 199 GLU cc_start: 0.4827 (tm-30) cc_final: 0.3698 (mp0) REVERT: B 535 LYS cc_start: 0.8643 (ttmt) cc_final: 0.7945 (ttmt) REVERT: B 583 GLU cc_start: 0.7374 (pm20) cc_final: 0.6853 (pm20) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0695 time to fit residues: 11.0635 Evaluate side-chains 107 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.0030 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- 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 ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.143206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119268 restraints weight = 8586.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123400 restraints weight = 5244.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126355 restraints weight = 3574.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.128464 restraints weight = 2611.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.129891 restraints weight = 2020.592| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.6987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4135 Z= 0.133 Angle : 0.635 7.766 5638 Z= 0.324 Chirality : 0.045 0.158 635 Planarity : 0.004 0.041 722 Dihedral : 5.406 35.522 559 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.36), residues: 516 helix: -1.27 (1.24), residues: 18 sheet: 0.79 (0.35), residues: 211 loop : -0.80 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 577 TYR 0.015 0.002 TYR F 34 PHE 0.009 0.001 PHE E 173 TRP 0.016 0.002 TRP E 161 HIS 0.004 0.001 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4130) covalent geometry : angle 0.63232 ( 5628) SS BOND : bond 0.00712 ( 5) SS BOND : angle 1.61191 ( 10) hydrogen bonds : bond 0.03226 ( 126) hydrogen bonds : angle 6.40945 ( 381) *********************** 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 137 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7508 (mt0) cc_final: 0.6233 (tm-30) REVERT: E 112 GLN cc_start: 0.7888 (tp40) cc_final: 0.7579 (tp-100) REVERT: F 4 LEU cc_start: 0.8726 (mt) cc_final: 0.8243 (mt) REVERT: F 78 ASN cc_start: 0.7892 (m-40) cc_final: 0.7603 (m-40) REVERT: F 79 ILE cc_start: 0.8185 (mm) cc_final: 0.7689 (mm) REVERT: F 92 CYS cc_start: 0.3275 (p) cc_final: 0.2278 (p) REVERT: F 96 ARG cc_start: 0.8494 (tpt90) cc_final: 0.7957 (tpt90) REVERT: F 179 MET cc_start: 0.7562 (tmm) cc_final: 0.7087 (tmm) REVERT: F 197 THR cc_start: 0.4604 (m) cc_final: 0.4319 (m) REVERT: F 199 GLU cc_start: 0.4869 (tm-30) cc_final: 0.3764 (mp0) REVERT: B 535 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8148 (tttt) REVERT: B 573 THR cc_start: 0.9139 (p) cc_final: 0.8833 (p) REVERT: B 583 GLU cc_start: 0.7447 (pm20) cc_final: 0.6845 (pm20) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0621 time to fit residues: 10.3463 Evaluate side-chains 110 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 0.0370 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.2660 ------------------------------------------------------------------------------- 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 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120078 restraints weight = 8733.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124295 restraints weight = 5239.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127298 restraints weight = 3519.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129482 restraints weight = 2552.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130983 restraints weight = 1954.849| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4135 Z= 0.128 Angle : 0.623 7.036 5638 Z= 0.315 Chirality : 0.045 0.218 635 Planarity : 0.005 0.045 722 Dihedral : 5.068 26.768 559 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.36), residues: 516 helix: -0.88 (1.49), residues: 12 sheet: 0.79 (0.35), residues: 211 loop : -0.82 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 577 TYR 0.019 0.002 TYR F 177 PHE 0.008 0.001 PHE E 173 TRP 0.017 0.002 TRP E 161 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4130) covalent geometry : angle 0.61956 ( 5628) SS BOND : bond 0.00754 ( 5) SS BOND : angle 1.57634 ( 10) hydrogen bonds : bond 0.03024 ( 126) hydrogen bonds : angle 5.95399 ( 381) *********************** 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 124 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7353 (mt0) cc_final: 0.6158 (tm-30) REVERT: E 35 ASN cc_start: 0.8369 (m-40) cc_final: 0.8118 (m-40) REVERT: E 112 GLN cc_start: 0.7954 (tp40) cc_final: 0.7594 (tp-100) REVERT: F 4 LEU cc_start: 0.8690 (mt) cc_final: 0.8379 (mt) REVERT: F 78 ASN cc_start: 0.7954 (m-40) cc_final: 0.7655 (m-40) REVERT: F 79 ILE cc_start: 0.8206 (mm) cc_final: 0.7719 (mm) REVERT: F 96 ARG cc_start: 0.8369 (tpt90) cc_final: 0.7900 (tpt90) REVERT: F 109 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6629 (tm-30) REVERT: F 179 MET cc_start: 0.7594 (tmm) cc_final: 0.7143 (tmm) REVERT: F 199 GLU cc_start: 0.4731 (tm-30) cc_final: 0.3685 (mp0) REVERT: B 535 LYS cc_start: 0.8821 (ttmt) cc_final: 0.7792 (ttmt) REVERT: B 583 GLU cc_start: 0.7444 (pm20) cc_final: 0.6887 (pm20) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0523 time to fit residues: 8.0329 Evaluate side-chains 107 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.118094 restraints weight = 8974.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122221 restraints weight = 5476.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125100 restraints weight = 3742.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127226 restraints weight = 2758.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128672 restraints weight = 2149.849| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4135 Z= 0.148 Angle : 0.649 6.994 5638 Z= 0.332 Chirality : 0.046 0.171 635 Planarity : 0.005 0.042 722 Dihedral : 5.235 27.497 559 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.84 % Favored : 94.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.36), residues: 516 helix: None (None), residues: 0 sheet: 0.74 (0.35), residues: 205 loop : -0.61 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 577 TYR 0.018 0.002 TYR F 53 PHE 0.009 0.001 PHE E 173 TRP 0.020 0.002 TRP E 161 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4130) covalent geometry : angle 0.64227 ( 5628) SS BOND : bond 0.00733 ( 5) SS BOND : angle 2.30385 ( 10) hydrogen bonds : bond 0.03205 ( 126) hydrogen bonds : angle 5.94197 ( 381) *********************** 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 127 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7354 (mt0) cc_final: 0.6156 (tm-30) REVERT: E 35 ASN cc_start: 0.8363 (m-40) cc_final: 0.8149 (m-40) REVERT: E 112 GLN cc_start: 0.8141 (tp40) cc_final: 0.7714 (tp-100) REVERT: F 4 LEU cc_start: 0.8714 (mt) cc_final: 0.8391 (mt) REVERT: F 78 ASN cc_start: 0.8024 (m-40) cc_final: 0.7753 (m-40) REVERT: F 79 ILE cc_start: 0.8265 (mm) cc_final: 0.7785 (mm) REVERT: F 92 CYS cc_start: 0.2531 (p) cc_final: 0.2277 (p) REVERT: F 96 ARG cc_start: 0.8419 (tpt90) cc_final: 0.7725 (tpt90) REVERT: F 109 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6610 (tm-30) REVERT: F 179 MET cc_start: 0.7597 (tmm) cc_final: 0.7056 (tmm) REVERT: F 197 THR cc_start: 0.4704 (m) cc_final: 0.4446 (m) REVERT: F 199 GLU cc_start: 0.4736 (tm-30) cc_final: 0.3736 (mp0) REVERT: B 535 LYS cc_start: 0.8576 (ttmt) cc_final: 0.7838 (ttmt) REVERT: B 559 PHE cc_start: 0.6351 (m-10) cc_final: 0.6049 (m-80) REVERT: B 573 THR cc_start: 0.9144 (p) cc_final: 0.7754 (p) REVERT: B 583 GLU cc_start: 0.7510 (pm20) cc_final: 0.6988 (pm20) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0559 time to fit residues: 8.8453 Evaluate side-chains 112 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 23 optimal weight: 0.0000 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.3962 ------------------------------------------------------------------------------- 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 52 HIS E 203 ASN F 46 GLN ** F 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.146580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122826 restraints weight = 8543.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126924 restraints weight = 5263.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.129778 restraints weight = 3602.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131951 restraints weight = 2649.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133478 restraints weight = 2050.627| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.7515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4135 Z= 0.106 Angle : 0.604 6.508 5638 Z= 0.308 Chirality : 0.046 0.158 635 Planarity : 0.004 0.040 722 Dihedral : 4.920 26.903 559 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.68 % Favored : 96.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.36), residues: 516 helix: -0.09 (2.47), residues: 6 sheet: 0.84 (0.36), residues: 190 loop : -0.61 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 567 TYR 0.012 0.001 TYR E 103 PHE 0.009 0.001 PHE B 592 TRP 0.020 0.002 TRP E 195 HIS 0.002 0.001 HIS F 202 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4130) covalent geometry : angle 0.59917 ( 5628) SS BOND : bond 0.00561 ( 5) SS BOND : angle 1.82576 ( 10) hydrogen bonds : bond 0.02950 ( 126) hydrogen bonds : angle 5.59645 ( 381) *********************** 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 127 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7548 (mt0) cc_final: 0.6296 (tm-30) REVERT: E 35 ASN cc_start: 0.8206 (m-40) cc_final: 0.7904 (m-40) REVERT: E 57 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6634 (mm-30) REVERT: E 112 GLN cc_start: 0.8126 (tp40) cc_final: 0.7896 (tp40) REVERT: F 4 LEU cc_start: 0.8724 (mt) cc_final: 0.8043 (tp) REVERT: F 78 ASN cc_start: 0.7869 (m-40) cc_final: 0.7660 (m-40) REVERT: F 79 ILE cc_start: 0.8164 (mm) cc_final: 0.7720 (mm) REVERT: F 92 CYS cc_start: 0.2742 (p) cc_final: 0.1235 (p) REVERT: F 96 ARG cc_start: 0.8296 (tpt90) cc_final: 0.7840 (tpt90) REVERT: F 109 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6735 (tm-30) REVERT: F 197 THR cc_start: 0.4780 (m) cc_final: 0.4413 (m) REVERT: F 199 GLU cc_start: 0.4727 (tm-30) cc_final: 0.3940 (mp0) REVERT: B 535 LYS cc_start: 0.8493 (ttmt) cc_final: 0.7811 (ttmt) REVERT: B 583 GLU cc_start: 0.7416 (pm20) cc_final: 0.6928 (pm20) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0577 time to fit residues: 9.0981 Evaluate side-chains 106 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 21 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 overall best weight: 2.5344 ------------------------------------------------------------------------------- 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 43 GLN E 203 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115904 restraints weight = 9009.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119746 restraints weight = 5628.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122561 restraints weight = 3912.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124567 restraints weight = 2925.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125980 restraints weight = 2308.875| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.7969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4135 Z= 0.194 Angle : 0.704 7.293 5638 Z= 0.361 Chirality : 0.046 0.167 635 Planarity : 0.005 0.041 722 Dihedral : 5.528 27.690 559 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.20 % Favored : 93.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.36), residues: 516 helix: -1.11 (2.87), residues: 6 sheet: 0.45 (0.35), residues: 201 loop : -0.58 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 328 TYR 0.025 0.003 TYR E 103 PHE 0.014 0.002 PHE E 173 TRP 0.021 0.003 TRP E 161 HIS 0.004 0.001 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 4130) covalent geometry : angle 0.69698 ( 5628) SS BOND : bond 0.00811 ( 5) SS BOND : angle 2.42010 ( 10) hydrogen bonds : bond 0.03509 ( 126) hydrogen bonds : angle 6.07743 ( 381) *********************** 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 to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7350 (mt0) cc_final: 0.6179 (tm-30) REVERT: E 81 MET cc_start: 0.8526 (mtp) cc_final: 0.8259 (mtp) REVERT: E 112 GLN cc_start: 0.8103 (tp40) cc_final: 0.7660 (tp-100) REVERT: F 4 LEU cc_start: 0.8739 (mt) cc_final: 0.8386 (mt) REVERT: F 78 ASN cc_start: 0.8046 (m-40) cc_final: 0.7789 (m-40) REVERT: F 79 ILE cc_start: 0.8133 (mm) cc_final: 0.7675 (mm) REVERT: F 92 CYS cc_start: 0.3000 (p) cc_final: 0.2770 (p) REVERT: F 96 ARG cc_start: 0.8358 (tpt90) cc_final: 0.7948 (tpt90) REVERT: F 97 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6156 (pm20) REVERT: F 179 MET cc_start: 0.7613 (tmm) cc_final: 0.7208 (tmm) REVERT: F 197 THR cc_start: 0.5130 (m) cc_final: 0.4925 (m) REVERT: F 199 GLU cc_start: 0.5079 (tm-30) cc_final: 0.4204 (mp0) REVERT: B 535 LYS cc_start: 0.8647 (ttmt) cc_final: 0.7939 (ttmt) REVERT: B 552 LEU cc_start: 0.8673 (mm) cc_final: 0.8442 (mm) REVERT: B 559 PHE cc_start: 0.6744 (m-10) cc_final: 0.6279 (m-80) REVERT: B 583 GLU cc_start: 0.7386 (pm20) cc_final: 0.6851 (pm20) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0531 time to fit residues: 8.1024 Evaluate side-chains 103 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.140755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.116798 restraints weight = 8852.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120649 restraints weight = 5550.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123489 restraints weight = 3875.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125535 restraints weight = 2869.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126946 restraints weight = 2253.812| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.8153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4135 Z= 0.181 Angle : 0.685 7.473 5638 Z= 0.351 Chirality : 0.046 0.145 635 Planarity : 0.005 0.040 722 Dihedral : 5.622 27.539 559 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.36), residues: 516 helix: -1.41 (2.65), residues: 6 sheet: 0.32 (0.35), residues: 200 loop : -0.72 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 577 TYR 0.018 0.002 TYR E 103 PHE 0.015 0.002 PHE E 173 TRP 0.021 0.003 TRP E 161 HIS 0.004 0.001 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 4130) covalent geometry : angle 0.67948 ( 5628) SS BOND : bond 0.00750 ( 5) SS BOND : angle 2.24823 ( 10) hydrogen bonds : bond 0.03543 ( 126) hydrogen bonds : angle 6.14673 ( 381) ********************** 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 122 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: E 5 GLN cc_start: 0.7355 (mt0) cc_final: 0.6213 (tm-30) REVERT: E 112 GLN cc_start: 0.8121 (tp40) cc_final: 0.7605 (tp-100) REVERT: F 4 LEU cc_start: 0.8761 (mt) cc_final: 0.8428 (mt) REVERT: F 37 MET cc_start: 0.7832 (tpp) cc_final: 0.7522 (tpp) REVERT: F 59 GLU cc_start: 0.7895 (tp30) cc_final: 0.7147 (tm-30) REVERT: F 78 ASN cc_start: 0.8155 (m-40) cc_final: 0.7916 (m-40) REVERT: F 79 ILE cc_start: 0.8219 (mm) cc_final: 0.7704 (mm) REVERT: F 92 CYS cc_start: 0.2948 (p) cc_final: 0.2696 (p) REVERT: F 96 ARG cc_start: 0.8447 (tpt90) cc_final: 0.7892 (tpt90) REVERT: F 179 MET cc_start: 0.7571 (tmm) cc_final: 0.7152 (tmm) REVERT: F 197 THR cc_start: 0.5104 (m) cc_final: 0.4755 (m) REVERT: F 199 GLU cc_start: 0.5070 (tm-30) cc_final: 0.4266 (mp0) REVERT: B 535 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8010 (ttmt) REVERT: B 559 PHE cc_start: 0.6620 (m-10) cc_final: 0.6148 (m-80) REVERT: B 583 GLU cc_start: 0.7499 (pm20) cc_final: 0.6930 (pm20) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0644 time to fit residues: 9.8799 Evaluate side-chains 108 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 chunk 50 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 170 GLN B 544 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.146371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.122127 restraints weight = 8679.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126183 restraints weight = 5390.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129123 restraints weight = 3712.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131326 restraints weight = 2734.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132926 restraints weight = 2114.495| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4135 Z= 0.103 Angle : 0.605 6.726 5638 Z= 0.307 Chirality : 0.045 0.155 635 Planarity : 0.005 0.040 722 Dihedral : 4.894 26.731 559 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.68 % Favored : 96.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.36), residues: 516 helix: -0.83 (1.65), residues: 12 sheet: 0.44 (0.36), residues: 190 loop : -0.63 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 577 TYR 0.009 0.001 TYR F 90 PHE 0.008 0.001 PHE B 541 TRP 0.024 0.002 TRP E 195 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 4130) covalent geometry : angle 0.60233 ( 5628) SS BOND : bond 0.00527 ( 5) SS BOND : angle 1.52265 ( 10) hydrogen bonds : bond 0.03011 ( 126) hydrogen bonds : angle 5.64730 ( 381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 800.76 seconds wall clock time: 14 minutes 32.60 seconds (872.60 seconds total)