Starting phenix.real_space_refine on Thu Nov 14 09:50:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/11_2024/8hc8_34655.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/11_2024/8hc8_34655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/11_2024/8hc8_34655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/11_2024/8hc8_34655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/11_2024/8hc8_34655.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/11_2024/8hc8_34655.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 809 atoms to isotropic. 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 22 5.16 5 C 3056 2.51 5 N 811 2.21 5 O 943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4832 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1508 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain: "H" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1734 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain: "L" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1576 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.58, per 1000 atoms: 0.74 Number of scatterers: 4832 At special positions: 0 Unit cell: (80.85, 90.75, 113.85, 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 22 16.00 O 943 8.00 N 811 7.00 C 3056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 626.3 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 14 sheets defined 7.0% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.833A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.526A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.885A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.753A pdb=" N LYS L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.679A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.727A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.244A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.508A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 20 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 82 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER H 75 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR H 73 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.563A pdb=" N TYR H 98 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 130 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 96 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 35 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.563A pdb=" N TYR H 98 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 130 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 96 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 102 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU H 123 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 141 through 144 removed outlier: 3.546A pdb=" N SER H 141 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 162 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 205 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 159 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL H 202 " --> pdb=" O HIS H 185 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 141 through 144 removed outlier: 3.546A pdb=" N SER H 141 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 162 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 205 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 159 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 190 " --> pdb=" O SER H 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 172 through 175 removed outlier: 3.706A pdb=" N CYS H 217 " --> pdb=" O LYS H 230 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS H 230 " --> pdb=" O CYS H 217 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 219 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL H 228 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS H 221 " --> pdb=" O THR H 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 226 " --> pdb=" O HIS H 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.897A pdb=" N CYS L 23 " --> pdb=" O PHE L 76 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE L 76 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 50 through 53 removed outlier: 5.748A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 90 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 121 through 123 removed outlier: 3.555A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 152 through 155 removed outlier: 3.861A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL L 201 " --> pdb=" O VAL L 210 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 237 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: 1.37 Time building geometry restraints manager: 1.30 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: 1552 1.35 - 1.46: 1248 1.46 - 1.58: 2124 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 4950 Sorted by residual: bond pdb=" C ALA C 372 " pdb=" N PRO C 373 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.23e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.47e+00 bond pdb=" CB PRO H 144 " pdb=" CG PRO H 144 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.96e+00 bond pdb=" CB GLU L 200 " pdb=" CG GLU L 200 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 4945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 6581 1.97 - 3.93: 128 3.93 - 5.90: 20 5.90 - 7.86: 9 7.86 - 9.83: 5 Bond angle restraints: 6743 Sorted by residual: angle pdb=" C TYR L 145 " pdb=" N PRO L 146 " pdb=" CA PRO L 146 " ideal model delta sigma weight residual 119.84 115.17 4.67 1.25e+00 6.40e-01 1.39e+01 angle pdb=" C PHE C 377 " pdb=" N LYS C 378 " pdb=" CA LYS C 378 " ideal model delta sigma weight residual 122.46 127.37 -4.91 1.41e+00 5.03e-01 1.21e+01 angle pdb=" CA PRO H 144 " pdb=" N PRO H 144 " pdb=" CD PRO H 144 " ideal model delta sigma weight residual 112.00 107.57 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.46 126.85 -4.39 1.41e+00 5.03e-01 9.69e+00 angle pdb=" N ILE L 111 " pdb=" CA ILE L 111 " pdb=" C ILE L 111 " ideal model delta sigma weight residual 109.12 113.87 -4.75 1.58e+00 4.01e-01 9.05e+00 ... (remaining 6738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2518 17.19 - 34.39: 332 34.39 - 51.58: 97 51.58 - 68.77: 10 68.77 - 85.97: 5 Dihedral angle restraints: 2962 sinusoidal: 1137 harmonic: 1825 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -32.64 -53.36 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual -86.00 -126.30 40.30 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA LEU L 141 " pdb=" C LEU L 141 " pdb=" N ASN L 142 " pdb=" CA ASN L 142 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 481 0.037 - 0.074: 184 0.074 - 0.111: 70 0.111 - 0.148: 14 0.148 - 0.185: 5 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA THR L 99 " pdb=" N THR L 99 " pdb=" C THR L 99 " pdb=" CB THR L 99 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CG LEU L 186 " pdb=" CB LEU L 186 " pdb=" CD1 LEU L 186 " pdb=" CD2 LEU L 186 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB ILE H 216 " pdb=" CA ILE H 216 " pdb=" CG1 ILE H 216 " pdb=" CG2 ILE H 216 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 134 " 0.027 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C SER H 134 " -0.092 2.00e-02 2.50e+03 pdb=" O SER H 134 " 0.034 2.00e-02 2.50e+03 pdb=" N ALA H 135 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 143 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO H 144 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO H 144 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 144 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 369 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR C 369 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR C 369 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 370 " -0.019 2.00e-02 2.50e+03 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1580 2.83 - 3.35: 3756 3.35 - 3.87: 7648 3.87 - 4.38: 7956 4.38 - 4.90: 14303 Nonbonded interactions: 35243 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.317 3.040 nonbonded pdb=" OG SER L 70 " pdb=" O THR L 77 " model vdw 2.371 3.040 nonbonded pdb=" OG SER L 187 " pdb=" OD2 ASP L 190 " model vdw 2.375 3.040 nonbonded pdb=" OH TYR H 63 " pdb=" O THR H 112 " model vdw 2.410 3.040 nonbonded pdb=" N ASN C 354 " pdb=" OD1 ASN C 354 " model vdw 2.415 3.120 ... (remaining 35238 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=0.00 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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 0.070 4950 Z= 0.207 Angle : 0.712 9.829 6743 Z= 0.363 Chirality : 0.046 0.185 754 Planarity : 0.007 0.122 871 Dihedral : 16.598 85.966 1772 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.56 % Allowed : 33.02 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.32), residues: 620 helix: -4.33 (0.50), residues: 20 sheet: 1.02 (0.43), residues: 161 loop : -1.42 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 175 HIS 0.002 0.001 HIS L 203 PHE 0.023 0.001 PHE C 456 TYR 0.031 0.001 TYR H 215 ARG 0.002 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.502 Fit side-chains REVERT: H 129 MET cc_start: 0.7128 (mmm) cc_final: 0.6401 (ppp) REVERT: H 177 SER cc_start: 0.6814 (m) cc_final: 0.6313 (t) outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.1509 time to fit residues: 16.6348 Evaluate side-chains 74 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 210 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4950 Z= 0.418 Angle : 0.726 9.737 6743 Z= 0.374 Chirality : 0.047 0.171 754 Planarity : 0.006 0.078 871 Dihedral : 4.804 26.633 708 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.86 % Allowed : 26.72 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.32), residues: 620 helix: -4.36 (0.43), residues: 41 sheet: 0.73 (0.42), residues: 160 loop : -1.41 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 436 HIS 0.003 0.001 HIS L 203 PHE 0.020 0.003 PHE H 121 TYR 0.038 0.003 TYR L 101 ARG 0.004 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.526 Fit side-chains REVERT: C 332 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.6060 (tt) REVERT: C 378 LYS cc_start: 0.8721 (pttt) cc_final: 0.8463 (pttt) REVERT: H 113 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7551 (p) REVERT: H 123 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8903 (tt) REVERT: L 138 VAL cc_start: 0.6326 (t) cc_final: 0.6106 (m) REVERT: L 154 LYS cc_start: 0.8605 (ptmt) cc_final: 0.8137 (pttm) outliers start: 37 outliers final: 22 residues processed: 107 average time/residue: 0.1631 time to fit residues: 22.5131 Evaluate side-chains 95 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 210 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4950 Z= 0.182 Angle : 0.554 7.046 6743 Z= 0.276 Chirality : 0.043 0.145 754 Planarity : 0.004 0.064 871 Dihedral : 3.956 18.659 708 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.12 % Allowed : 27.09 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.32), residues: 620 helix: -4.28 (0.50), residues: 38 sheet: 0.74 (0.42), residues: 162 loop : -1.19 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS C 505 PHE 0.010 0.001 PHE C 342 TYR 0.010 0.001 TYR L 101 ARG 0.003 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.474 Fit side-chains REVERT: L 154 LYS cc_start: 0.8509 (ptmt) cc_final: 0.8055 (pttt) outliers start: 33 outliers final: 20 residues processed: 108 average time/residue: 0.1508 time to fit residues: 21.4625 Evaluate side-chains 93 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4950 Z= 0.237 Angle : 0.575 7.497 6743 Z= 0.289 Chirality : 0.043 0.175 754 Planarity : 0.004 0.055 871 Dihedral : 3.923 19.098 707 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 7.61 % Allowed : 26.72 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.32), residues: 620 helix: -4.14 (0.52), residues: 39 sheet: 0.61 (0.41), residues: 165 loop : -1.17 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 153 HIS 0.001 0.000 HIS L 203 PHE 0.012 0.002 PHE C 429 TYR 0.013 0.001 TYR L 101 ARG 0.005 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.601 Fit side-chains REVERT: C 392 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8179 (p90) REVERT: H 123 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8953 (tt) REVERT: H 215 TYR cc_start: 0.4685 (m-10) cc_final: 0.4389 (m-10) REVERT: L 154 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8139 (pttt) outliers start: 41 outliers final: 27 residues processed: 109 average time/residue: 0.1716 time to fit residues: 23.9850 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 40.0000 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN H 218 ASN L 6 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 4950 Z= 0.418 Angle : 0.688 9.280 6743 Z= 0.352 Chirality : 0.046 0.198 754 Planarity : 0.005 0.049 871 Dihedral : 4.649 21.121 707 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 9.09 % Allowed : 25.42 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.32), residues: 620 helix: -4.05 (0.54), residues: 40 sheet: 0.26 (0.41), residues: 165 loop : -1.46 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 436 HIS 0.002 0.001 HIS C 505 PHE 0.023 0.003 PHE L 103 TYR 0.029 0.002 TYR L 101 ARG 0.007 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 81 time to evaluate : 0.553 Fit side-chains REVERT: C 355 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8669 (ttm-80) REVERT: C 392 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7866 (p90) REVERT: C 516 GLU cc_start: 0.7286 (pm20) cc_final: 0.7036 (pm20) REVERT: H 106 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8786 (ttt90) REVERT: H 123 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9179 (tt) REVERT: H 215 TYR cc_start: 0.5522 (m-10) cc_final: 0.5121 (m-10) outliers start: 49 outliers final: 35 residues processed: 120 average time/residue: 0.1963 time to fit residues: 29.2544 Evaluate side-chains 112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4950 Z= 0.239 Angle : 0.592 8.593 6743 Z= 0.297 Chirality : 0.044 0.170 754 Planarity : 0.004 0.047 871 Dihedral : 4.201 20.951 707 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 8.35 % Allowed : 25.97 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.32), residues: 620 helix: -3.98 (0.52), residues: 40 sheet: 0.30 (0.40), residues: 165 loop : -1.38 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 436 HIS 0.001 0.000 HIS H 221 PHE 0.013 0.002 PHE L 103 TYR 0.010 0.001 TYR L 91 ARG 0.006 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 0.556 Fit side-chains REVERT: C 355 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8693 (ttm-80) REVERT: C 392 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7868 (p90) REVERT: C 516 GLU cc_start: 0.7212 (pm20) cc_final: 0.6922 (pm20) REVERT: H 123 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9002 (tt) REVERT: H 215 TYR cc_start: 0.5540 (m-10) cc_final: 0.5123 (m-10) outliers start: 45 outliers final: 27 residues processed: 120 average time/residue: 0.1830 time to fit residues: 27.6209 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 50.0000 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4950 Z= 0.297 Angle : 0.616 8.972 6743 Z= 0.311 Chirality : 0.045 0.188 754 Planarity : 0.004 0.046 871 Dihedral : 4.294 21.303 707 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 8.16 % Allowed : 26.35 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.32), residues: 620 helix: -3.98 (0.53), residues: 40 sheet: 0.25 (0.41), residues: 165 loop : -1.41 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 175 HIS 0.001 0.000 HIS C 505 PHE 0.016 0.002 PHE L 103 TYR 0.019 0.002 TYR L 101 ARG 0.007 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 0.446 Fit side-chains REVERT: C 355 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8696 (ttm-80) REVERT: C 392 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7843 (p90) REVERT: C 516 GLU cc_start: 0.7362 (pm20) cc_final: 0.7017 (pm20) REVERT: H 123 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9024 (tt) REVERT: H 215 TYR cc_start: 0.5237 (m-10) cc_final: 0.4841 (m-10) outliers start: 44 outliers final: 32 residues processed: 114 average time/residue: 0.1796 time to fit residues: 25.8829 Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4950 Z= 0.194 Angle : 0.578 8.345 6743 Z= 0.289 Chirality : 0.044 0.204 754 Planarity : 0.004 0.046 871 Dihedral : 4.054 20.752 707 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 6.49 % Allowed : 27.83 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.32), residues: 620 helix: -3.95 (0.56), residues: 38 sheet: 0.30 (0.40), residues: 165 loop : -1.24 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 153 HIS 0.001 0.000 HIS H 221 PHE 0.012 0.002 PHE C 486 TYR 0.010 0.001 TYR L 91 ARG 0.005 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.487 Fit side-chains REVERT: C 355 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8619 (ttm-80) REVERT: C 392 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7975 (p90) REVERT: C 516 GLU cc_start: 0.7312 (pm20) cc_final: 0.6983 (pm20) REVERT: H 215 TYR cc_start: 0.5171 (m-10) cc_final: 0.4805 (m-10) outliers start: 35 outliers final: 28 residues processed: 104 average time/residue: 0.1915 time to fit residues: 24.9520 Evaluate side-chains 102 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.0000 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 60 optimal weight: 0.0570 overall best weight: 0.1646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4950 Z= 0.141 Angle : 0.547 7.688 6743 Z= 0.271 Chirality : 0.043 0.212 754 Planarity : 0.004 0.047 871 Dihedral : 3.691 18.664 707 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.34 % Allowed : 31.35 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.33), residues: 620 helix: -3.82 (0.59), residues: 37 sheet: 0.68 (0.42), residues: 156 loop : -1.09 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 153 HIS 0.001 0.000 HIS H 221 PHE 0.012 0.001 PHE C 486 TYR 0.009 0.001 TYR L 91 ARG 0.004 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.553 Fit side-chains REVERT: C 392 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8106 (p90) REVERT: H 215 TYR cc_start: 0.5830 (m-10) cc_final: 0.5456 (m-10) REVERT: H 227 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7221 (mmmt) outliers start: 18 outliers final: 14 residues processed: 91 average time/residue: 0.1957 time to fit residues: 22.4931 Evaluate side-chains 91 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS L 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4950 Z= 0.174 Angle : 0.559 7.608 6743 Z= 0.277 Chirality : 0.043 0.217 754 Planarity : 0.004 0.045 871 Dihedral : 3.728 19.484 707 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.97 % Allowed : 31.54 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.33), residues: 620 helix: -3.49 (0.70), residues: 32 sheet: 0.54 (0.41), residues: 161 loop : -1.05 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.002 0.000 HIS H 221 PHE 0.013 0.001 PHE C 342 TYR 0.008 0.001 TYR L 91 ARG 0.005 0.000 ARG H 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.545 Fit side-chains REVERT: C 392 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8110 (p90) REVERT: H 215 TYR cc_start: 0.5821 (m-10) cc_final: 0.5431 (m-10) outliers start: 16 outliers final: 14 residues processed: 85 average time/residue: 0.2048 time to fit residues: 21.9347 Evaluate side-chains 88 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.0070 chunk 35 optimal weight: 0.0870 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS ** H 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.181219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172787 restraints weight = 6314.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171851 restraints weight = 13959.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.160293 restraints weight = 14186.117| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 4950 Z= 0.265 Angle : 1.141 59.183 6743 Z= 0.684 Chirality : 0.043 0.202 754 Planarity : 0.004 0.045 871 Dihedral : 3.813 23.120 707 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.15 % Allowed : 31.17 % Favored : 65.68 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.33), residues: 620 helix: -3.49 (0.70), residues: 32 sheet: 0.54 (0.41), residues: 161 loop : -1.06 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.002 0.000 HIS H 221 PHE 0.013 0.001 PHE C 342 TYR 0.017 0.001 TYR L 37 ARG 0.003 0.000 ARG H 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.26 seconds wall clock time: 25 minutes 59.15 seconds (1559.15 seconds total)