Starting phenix.real_space_refine on Thu Dec 7 21:00:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2m_28822/12_2023/8f2m_28822.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2m_28822/12_2023/8f2m_28822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2m_28822/12_2023/8f2m_28822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2m_28822/12_2023/8f2m_28822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2m_28822/12_2023/8f2m_28822.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2m_28822/12_2023/8f2m_28822.pdb" } resolution = 3.7 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= 0.001 sd= 0.010 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 9 5.16 5 C 2970 2.51 5 N 794 2.21 5 O 923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 16": "OE1" <-> "OE2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D ASP 187": "OD1" <-> "OD2" Residue "D TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F ASP 45": "OD1" <-> "OD2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ASP 10": "OD1" <-> "OD2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4696 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3425 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Chain: "F" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 589 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "B" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 589 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 93 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Time building chain proxies: 2.92, per 1000 atoms: 0.62 Number of scatterers: 4696 At special positions: 0 Unit cell: (101.556, 108.108, 126.672, 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 9 16.00 O 923 8.00 N 794 7.00 C 2970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 840.0 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 6 sheets defined 45.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.748A pdb=" N TYR D 18 " --> pdb=" O THR D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 54 through 78 removed outlier: 3.625A pdb=" N ILE D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 111 through 118 removed outlier: 3.743A pdb=" N GLN D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 157 through 192 removed outlier: 3.703A pdb=" N ASN D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 225 removed outlier: 3.548A pdb=" N THR D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.673A pdb=" N GLU D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 268 removed outlier: 4.554A pdb=" N LEU D 264 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'F' and resid 4 through 15 removed outlier: 3.601A pdb=" N ASP F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 74 removed outlier: 3.789A pdb=" N LEU F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA F 55 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.649A pdb=" N ILE B 11 " --> pdb=" O GLU B 7 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 12 " --> pdb=" O HIS B 8 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 13 " --> pdb=" O GLU B 9 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 73 removed outlier: 3.954A pdb=" N THR B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 54 " --> pdb=" O HIS B 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 87 through 90 removed outlier: 5.044A pdb=" N ASP D 304 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN D 90 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N LEU D 306 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP D 327 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS D 307 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N HIS D 325 " --> pdb=" O HIS D 307 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 138 " --> pdb=" O VAL D 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.684A pdb=" N TYR D 319 " --> pdb=" O ASN D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 279 through 282 Processing sheet with id=AA4, first strand: chain 'D' and resid 349 through 354 removed outlier: 4.419A pdb=" N GLN D 351 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 374 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 358 through 361 removed outlier: 5.988A pdb=" N ALA D 359 " --> pdb=" O SER D 436 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 429 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 366 through 368 removed outlier: 3.632A pdb=" N ALA D 395 " --> pdb=" O SER D 403 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 654 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: 1.20 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1563 1.34 - 1.46: 693 1.46 - 1.57: 2500 1.57 - 1.69: 1 1.69 - 1.81: 18 Bond restraints: 4775 Sorted by residual: bond pdb=" CB PRO D 356 " pdb=" CG PRO D 356 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.13e+00 bond pdb=" C SER D 355 " pdb=" N PRO D 356 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.89e+00 bond pdb=" CG PRO B 18 " pdb=" CD PRO B 18 " ideal model delta sigma weight residual 1.503 1.544 -0.041 3.40e-02 8.65e+02 1.43e+00 bond pdb=" CG PRO D 356 " pdb=" CD PRO D 356 " ideal model delta sigma weight residual 1.503 1.544 -0.041 3.40e-02 8.65e+02 1.43e+00 bond pdb=" CB LYS D 215 " pdb=" CG LYS D 215 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 ... (remaining 4770 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.93: 99 106.93 - 113.70: 2688 113.70 - 120.47: 1793 120.47 - 127.24: 1850 127.24 - 134.00: 37 Bond angle restraints: 6467 Sorted by residual: angle pdb=" CA PRO D 356 " pdb=" N PRO D 356 " pdb=" CD PRO D 356 " ideal model delta sigma weight residual 112.00 106.76 5.24 1.40e+00 5.10e-01 1.40e+01 angle pdb=" CA LYS D 223 " pdb=" CB LYS D 223 " pdb=" CG LYS D 223 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CB LYS D 215 " pdb=" CG LYS D 215 " pdb=" CD LYS D 215 " ideal model delta sigma weight residual 111.30 118.76 -7.46 2.30e+00 1.89e-01 1.05e+01 angle pdb=" N SER D 34 " pdb=" CA SER D 34 " pdb=" C SER D 34 " ideal model delta sigma weight residual 114.39 109.85 4.54 1.45e+00 4.76e-01 9.81e+00 angle pdb=" C TYR D 18 " pdb=" N ASP D 19 " pdb=" CA ASP D 19 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.21e+00 ... (remaining 6462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 2491 17.70 - 35.41: 306 35.41 - 53.11: 81 53.11 - 70.81: 12 70.81 - 88.52: 2 Dihedral angle restraints: 2892 sinusoidal: 1160 harmonic: 1732 Sorted by residual: dihedral pdb=" CA TYR D 18 " pdb=" C TYR D 18 " pdb=" N ASP D 19 " pdb=" CA ASP D 19 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA SER D 355 " pdb=" C SER D 355 " pdb=" N PRO D 356 " pdb=" CA PRO D 356 " ideal model delta harmonic sigma weight residual 180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE D 170 " pdb=" C ILE D 170 " pdb=" N TYR D 171 " pdb=" CA TYR D 171 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 534 0.038 - 0.075: 154 0.075 - 0.112: 46 0.112 - 0.150: 10 0.150 - 0.187: 2 Chirality restraints: 746 Sorted by residual: chirality pdb=" CA PRO D 356 " pdb=" N PRO D 356 " pdb=" C PRO D 356 " pdb=" CB PRO D 356 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA PRO B 18 " pdb=" N PRO B 18 " pdb=" C PRO B 18 " pdb=" CB PRO B 18 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ASP D 19 " pdb=" N ASP D 19 " pdb=" C ASP D 19 " pdb=" CB ASP D 19 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 743 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 355 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO D 356 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 226 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO D 227 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 227 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 227 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 4 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 5 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 5 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 5 " -0.021 5.00e-02 4.00e+02 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1022 2.78 - 3.31: 4429 3.31 - 3.84: 7211 3.84 - 4.37: 8206 4.37 - 4.90: 13799 Nonbonded interactions: 34667 Sorted by model distance: nonbonded pdb=" NZ LYS D 87 " pdb=" OE2 GLU D 178 " model vdw 2.253 2.520 nonbonded pdb=" OG SER D 11 " pdb=" OG SER D 17 " model vdw 2.255 2.440 nonbonded pdb=" OG SER D 405 " pdb=" OE2 GLU D 408 " model vdw 2.262 2.440 nonbonded pdb=" O GLY D 390 " pdb=" ND2 ASN D 410 " model vdw 2.266 2.520 nonbonded pdb=" OG1 THR D 15 " pdb=" OE2 GLU D 160 " model vdw 2.268 2.440 ... (remaining 34662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' } 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: 0.560 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: 2.400 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 17.480 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 4775 Z= 0.196 Angle : 0.671 7.461 6467 Z= 0.380 Chirality : 0.040 0.187 746 Planarity : 0.006 0.124 834 Dihedral : 16.382 88.515 1768 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 1.03 % Allowed : 4.98 % Favored : 93.99 % Rotamer: Outliers : 0.38 % Allowed : 24.18 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.34), residues: 582 helix: 0.70 (0.32), residues: 256 sheet: -0.62 (0.47), residues: 115 loop : -2.10 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 320 HIS 0.003 0.001 HIS D 248 PHE 0.019 0.001 PHE D 162 TYR 0.019 0.002 TYR D 324 ARG 0.008 0.001 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.1917 time to fit residues: 21.0388 Evaluate side-chains 70 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0518 time to fit residues: 0.9368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN F 22 GLN F 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4775 Z= 0.336 Angle : 0.695 8.416 6467 Z= 0.380 Chirality : 0.045 0.169 746 Planarity : 0.007 0.128 834 Dihedral : 5.306 27.988 633 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.19 % Favored : 92.96 % Rotamer: Outliers : 4.22 % Allowed : 20.92 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.34), residues: 582 helix: 0.97 (0.31), residues: 261 sheet: -0.68 (0.45), residues: 126 loop : -2.28 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 299 HIS 0.007 0.002 HIS D 141 PHE 0.039 0.003 PHE F 68 TYR 0.017 0.003 TYR F 36 ARG 0.005 0.001 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.545 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 102 average time/residue: 0.1714 time to fit residues: 22.2615 Evaluate side-chains 80 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0510 time to fit residues: 1.8206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 50.0000 chunk 14 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN F 8 HIS F 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 4775 Z= 0.175 Angle : 0.582 7.665 6467 Z= 0.319 Chirality : 0.042 0.171 746 Planarity : 0.006 0.125 834 Dihedral : 4.884 27.597 633 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.50 % Favored : 93.64 % Rotamer: Outliers : 1.54 % Allowed : 23.22 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.35), residues: 582 helix: 1.45 (0.32), residues: 251 sheet: -0.57 (0.47), residues: 126 loop : -2.26 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 299 HIS 0.004 0.001 HIS D 307 PHE 0.021 0.001 PHE F 68 TYR 0.016 0.002 TYR D 101 ARG 0.004 0.000 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.538 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 81 average time/residue: 0.1892 time to fit residues: 19.2789 Evaluate side-chains 68 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0547 time to fit residues: 1.0300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 50.0000 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 GLN D 234 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN D 337 ASN F 22 GLN B 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 4775 Z= 0.368 Angle : 0.691 7.659 6467 Z= 0.382 Chirality : 0.046 0.188 746 Planarity : 0.006 0.129 834 Dihedral : 5.567 31.865 633 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.87 % Favored : 92.10 % Rotamer: Outliers : 4.22 % Allowed : 21.31 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 (0.34), residues: 582 helix: 1.03 (0.31), residues: 268 sheet: -0.81 (0.46), residues: 126 loop : -2.37 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 299 HIS 0.006 0.002 HIS D 141 PHE 0.029 0.002 PHE D 162 TYR 0.017 0.002 TYR D 140 ARG 0.004 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 89 average time/residue: 0.1513 time to fit residues: 17.8607 Evaluate side-chains 75 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.551 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.0731 time to fit residues: 1.9803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.0050 chunk 0 optimal weight: 10.9990 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4775 Z= 0.204 Angle : 0.600 8.174 6467 Z= 0.327 Chirality : 0.043 0.180 746 Planarity : 0.006 0.126 834 Dihedral : 5.072 30.734 633 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 1.03 % Allowed : 5.15 % Favored : 93.81 % Rotamer: Outliers : 0.77 % Allowed : 23.42 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 (0.34), residues: 582 helix: 1.33 (0.31), residues: 265 sheet: -0.58 (0.47), residues: 123 loop : -2.38 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 299 HIS 0.004 0.001 HIS F 8 PHE 0.018 0.001 PHE D 162 TYR 0.015 0.001 TYR D 140 ARG 0.002 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.545 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.1614 time to fit residues: 15.6917 Evaluate side-chains 64 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.557 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0476 time to fit residues: 1.0194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 4775 Z= 0.288 Angle : 0.642 8.706 6467 Z= 0.353 Chirality : 0.044 0.184 746 Planarity : 0.006 0.126 834 Dihedral : 5.209 31.464 633 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.87 % Favored : 92.10 % Rotamer: Outliers : 2.30 % Allowed : 22.26 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 (0.35), residues: 582 helix: 1.17 (0.30), residues: 271 sheet: -0.66 (0.50), residues: 118 loop : -2.32 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 299 HIS 0.004 0.001 HIS F 8 PHE 0.025 0.002 PHE D 162 TYR 0.015 0.002 TYR D 140 ARG 0.004 0.000 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.573 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 87 average time/residue: 0.1512 time to fit residues: 17.5912 Evaluate side-chains 71 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0611 time to fit residues: 1.3106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 0.0170 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 overall best weight: 3.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4775 Z= 0.281 Angle : 0.661 9.019 6467 Z= 0.364 Chirality : 0.045 0.239 746 Planarity : 0.006 0.126 834 Dihedral : 5.226 31.776 633 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.53 % Favored : 92.44 % Rotamer: Outliers : 1.54 % Allowed : 23.99 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.57 (0.35), residues: 582 helix: 1.08 (0.30), residues: 271 sheet: -0.64 (0.48), residues: 123 loop : -2.36 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 299 HIS 0.003 0.001 HIS F 8 PHE 0.023 0.002 PHE D 162 TYR 0.014 0.002 TYR D 140 ARG 0.002 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.564 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.1496 time to fit residues: 15.7318 Evaluate side-chains 74 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0484 time to fit residues: 1.3088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4775 Z= 0.333 Angle : 0.691 8.516 6467 Z= 0.378 Chirality : 0.046 0.228 746 Planarity : 0.006 0.126 834 Dihedral : 5.438 32.872 633 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.22 % Favored : 91.75 % Rotamer: Outliers : 1.15 % Allowed : 23.61 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.18 % 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: -0.66 (0.35), residues: 582 helix: 1.04 (0.30), residues: 265 sheet: -0.71 (0.50), residues: 118 loop : -2.30 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 299 HIS 0.004 0.001 HIS B 50 PHE 0.026 0.002 PHE D 162 TYR 0.014 0.002 TYR D 322 ARG 0.003 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.540 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.1663 time to fit residues: 17.6559 Evaluate side-chains 77 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0483 time to fit residues: 1.1299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 4775 Z= 0.446 Angle : 0.772 8.251 6467 Z= 0.425 Chirality : 0.049 0.244 746 Planarity : 0.006 0.128 834 Dihedral : 5.898 34.606 633 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.90 % Favored : 91.07 % Rotamer: Outliers : 0.38 % Allowed : 25.34 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.18 % 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: -0.95 (0.35), residues: 582 helix: 0.87 (0.31), residues: 256 sheet: -0.90 (0.49), residues: 118 loop : -2.38 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 299 HIS 0.006 0.002 HIS B 50 PHE 0.027 0.002 PHE D 162 TYR 0.014 0.002 TYR D 322 ARG 0.004 0.001 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.572 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 0.1654 time to fit residues: 16.6959 Evaluate side-chains 71 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0477 time to fit residues: 0.9284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4775 Z= 0.294 Angle : 0.708 10.131 6467 Z= 0.388 Chirality : 0.046 0.247 746 Planarity : 0.006 0.126 834 Dihedral : 5.538 33.746 633 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.04 % Favored : 91.92 % Rotamer: Outliers : 0.19 % Allowed : 25.34 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.18 % 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: -0.81 (0.35), residues: 582 helix: 1.03 (0.31), residues: 255 sheet: -0.91 (0.49), residues: 118 loop : -2.30 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 299 HIS 0.004 0.001 HIS B 50 PHE 0.022 0.002 PHE D 162 TYR 0.013 0.002 TYR D 140 ARG 0.003 0.000 ARG D 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.547 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.1608 time to fit residues: 16.4100 Evaluate side-chains 71 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128791 restraints weight = 7103.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127724 restraints weight = 16220.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128149 restraints weight = 14419.039| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4775 Z= 0.346 Angle : 0.730 8.489 6467 Z= 0.400 Chirality : 0.047 0.247 746 Planarity : 0.006 0.126 834 Dihedral : 5.613 33.817 633 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 1.03 % Allowed : 8.25 % Favored : 90.72 % Rotamer: Outliers : 0.58 % Allowed : 25.34 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.18 % 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: -0.93 (0.35), residues: 582 helix: 0.76 (0.31), residues: 265 sheet: -0.87 (0.49), residues: 118 loop : -2.33 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 299 HIS 0.005 0.001 HIS B 50 PHE 0.025 0.002 PHE D 162 TYR 0.013 0.002 TYR D 140 ARG 0.003 0.000 ARG D 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1117.15 seconds wall clock time: 21 minutes 5.87 seconds (1265.87 seconds total)