Starting phenix.real_space_refine on Sat Dec 9 01:14:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/12_2023/5fn5_3240.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/12_2023/5fn5_3240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/12_2023/5fn5_3240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/12_2023/5fn5_3240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/12_2023/5fn5_3240.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn5_3240/12_2023/5fn5_3240.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 36 5.16 5 C 6313 2.51 5 N 1572 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9645 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627} Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1735 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 215} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 233} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 820 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.56, per 1000 atoms: 0.58 Number of scatterers: 9645 At special positions: 0 Unit cell: (93.8, 142.8, 96.6, 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 36 16.00 O 1724 8.00 N 1572 7.00 C 6313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.02 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.07 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.04 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: 4.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 59.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.842A pdb=" N ARG A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.892A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.198A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.666A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 removed outlier: 4.025A pdb=" N ARG A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.065A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 504 removed outlier: 3.570A pdb=" N GLY A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.733A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 561 through 575 removed outlier: 3.541A pdb=" N VAL A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 665 through 698 removed outlier: 5.173A pdb=" N ASP A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 102 Proline residue: B 88 - end of helix removed outlier: 3.509A pdb=" N LEU B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 190 removed outlier: 3.676A pdb=" N PHE B 179 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 180 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 244 through 263 Processing helix chain 'B' and resid 382 through 398 Processing helix chain 'B' and resid 403 through 429 removed outlier: 3.699A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 464 removed outlier: 3.675A pdb=" N VAL B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'C' and resid 2 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 60 removed outlier: 3.557A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 114 through 142 removed outlier: 3.654A pdb=" N SER C 129 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.510A pdb=" N PHE C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 3.939A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.759A pdb=" N ILE C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.590A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.801A pdb=" N ASN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 42 removed outlier: 3.782A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 Processing helix chain 'D' and resid 55 through 82 Processing helix chain 'D' and resid 86 through 92 Processing sheet with id= AA, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.559A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 59 through 60 Processing sheet with id= AC, first strand: chain 'A' and resid 413 through 414 removed outlier: 3.543A pdb=" N VAL A 440 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 413 through 414 removed outlier: 3.543A pdb=" N VAL A 440 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 361 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A 257 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 437 through 438 removed outlier: 6.800A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 603 through 604 Processing sheet with id= BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.969A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1671 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: 2.93 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1599 1.32 - 1.45: 2853 1.45 - 1.58: 5376 1.58 - 1.71: 12 1.71 - 1.83: 54 Bond restraints: 9894 Sorted by residual: bond pdb=" CA SER B 401 " pdb=" C SER B 401 " ideal model delta sigma weight residual 1.523 1.608 -0.084 1.34e-02 5.57e+03 3.97e+01 bond pdb=" N LEU C 243 " pdb=" CA LEU C 243 " ideal model delta sigma weight residual 1.457 1.528 -0.070 1.29e-02 6.01e+03 2.98e+01 bond pdb=" CA VAL A 579 " pdb=" C VAL A 579 " ideal model delta sigma weight residual 1.520 1.578 -0.058 1.07e-02 8.73e+03 2.95e+01 bond pdb=" CA LEU B 452 " pdb=" C LEU B 452 " ideal model delta sigma weight residual 1.525 1.476 0.050 1.02e-02 9.61e+03 2.37e+01 bond pdb=" CA LEU C 243 " pdb=" C LEU C 243 " ideal model delta sigma weight residual 1.523 1.582 -0.059 1.34e-02 5.57e+03 1.95e+01 ... (remaining 9889 not shown) Histogram of bond angle deviations from ideal: 98.93 - 106.01: 262 106.01 - 113.08: 4742 113.08 - 120.15: 3962 120.15 - 127.22: 4404 127.22 - 134.29: 118 Bond angle restraints: 13488 Sorted by residual: angle pdb=" N VAL C 120 " pdb=" CA VAL C 120 " pdb=" CB VAL C 120 " ideal model delta sigma weight residual 110.55 119.51 -8.96 1.17e+00 7.31e-01 5.87e+01 angle pdb=" N GLY A 547 " pdb=" CA GLY A 547 " pdb=" C GLY A 547 " ideal model delta sigma weight residual 112.57 102.37 10.20 1.37e+00 5.33e-01 5.54e+01 angle pdb=" N ALA B 400 " pdb=" CA ALA B 400 " pdb=" C ALA B 400 " ideal model delta sigma weight residual 109.40 121.49 -12.09 1.63e+00 3.76e-01 5.50e+01 angle pdb=" CA PHE C 88 " pdb=" C PHE C 88 " pdb=" N ALA C 89 " ideal model delta sigma weight residual 117.07 108.95 8.12 1.14e+00 7.69e-01 5.07e+01 angle pdb=" C ILE B 387 " pdb=" CA ILE B 387 " pdb=" CB ILE B 387 " ideal model delta sigma weight residual 111.97 102.87 9.10 1.28e+00 6.10e-01 5.06e+01 ... (remaining 13483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4792 17.40 - 34.79: 691 34.79 - 52.19: 221 52.19 - 69.59: 57 69.59 - 86.99: 10 Dihedral angle restraints: 5771 sinusoidal: 2196 harmonic: 3575 Sorted by residual: dihedral pdb=" CA ALA B 400 " pdb=" C ALA B 400 " pdb=" N SER B 401 " pdb=" CA SER B 401 " ideal model delta harmonic sigma weight residual -180.00 -128.06 -51.94 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 179.99 -86.99 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CA TYR B 106 " pdb=" C TYR B 106 " pdb=" N THR B 107 " pdb=" CA THR B 107 " ideal model delta harmonic sigma weight residual 180.00 132.58 47.42 0 5.00e+00 4.00e-02 8.99e+01 ... (remaining 5768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1341 0.151 - 0.301: 185 0.301 - 0.452: 26 0.452 - 0.602: 6 0.602 - 0.753: 2 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA PHE A 218 " pdb=" N PHE A 218 " pdb=" C PHE A 218 " pdb=" CB PHE A 218 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA PHE A 302 " pdb=" N PHE A 302 " pdb=" C PHE A 302 " pdb=" CB PHE A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CA TYR B 225 " pdb=" N TYR B 225 " pdb=" C TYR B 225 " pdb=" CB TYR B 225 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.45e+00 ... (remaining 1557 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " 0.072 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO A 560 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 87 " 0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO B 88 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " 0.038 2.00e-02 2.50e+03 2.64e-02 1.22e+01 pdb=" CG PHE B 388 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " 0.011 2.00e-02 2.50e+03 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 132 2.64 - 3.20: 9550 3.20 - 3.77: 16000 3.77 - 4.33: 20541 4.33 - 4.90: 33144 Nonbonded interactions: 79367 Sorted by model distance: nonbonded pdb=" O ILE C 34 " pdb=" OH TYR C 90 " model vdw 2.074 2.440 nonbonded pdb=" O ALA B 396 " pdb=" OG1 THR B 399 " model vdw 2.219 2.440 nonbonded pdb=" O LEU A 397 " pdb=" OG1 THR A 400 " model vdw 2.247 2.440 nonbonded pdb=" O LEU C 35 " pdb=" OG SER C 124 " model vdw 2.263 2.440 nonbonded pdb=" O ALA C 76 " pdb=" OG SER C 79 " model vdw 2.280 2.440 ... (remaining 79362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.830 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.590 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 : 0.012 0.095 9894 Z= 0.780 Angle : 1.850 12.870 13488 Z= 1.292 Chirality : 0.113 0.753 1560 Planarity : 0.008 0.110 1680 Dihedral : 18.823 81.957 3448 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 4.30 % Allowed : 11.41 % Favored : 84.28 % Rotamer: Outliers : 14.00 % Allowed : 16.49 % Favored : 69.51 % Cbeta Deviations : 2.43 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % Twisted General : 1.29 % 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: -1.91 (0.22), residues: 1209 helix: 1.07 (0.16), residues: 660 sheet: -3.39 (0.45), residues: 100 loop : -4.58 (0.22), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 36 HIS 0.013 0.003 HIS A 74 PHE 0.059 0.005 PHE A 302 TYR 0.042 0.004 TYR B 225 ARG 0.008 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 240 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 47 residues processed: 346 average time/residue: 0.2197 time to fit residues: 105.1541 Evaluate side-chains 198 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 1.208 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 47 outliers final: 1 residues processed: 47 average time/residue: 0.1583 time to fit residues: 12.7566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 535 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9894 Z= 0.282 Angle : 0.871 10.380 13488 Z= 0.454 Chirality : 0.048 0.209 1560 Planarity : 0.006 0.091 1680 Dihedral : 7.287 35.705 1319 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.77 % Favored : 90.07 % Rotamer: Outliers : 0.96 % Allowed : 6.14 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 3.70 % Twisted General : 0.09 % 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: -0.72 (0.25), residues: 1209 helix: 1.75 (0.20), residues: 694 sheet: -2.94 (0.44), residues: 110 loop : -3.97 (0.25), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 257 HIS 0.009 0.002 HIS A 553 PHE 0.035 0.003 PHE A 302 TYR 0.023 0.002 TYR C 69 ARG 0.006 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 216 average time/residue: 0.1879 time to fit residues: 59.8084 Evaluate side-chains 141 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1160 time to fit residues: 1.8019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 428 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 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 : 0.004 0.066 9894 Z= 0.295 Angle : 0.796 10.054 13488 Z= 0.415 Chirality : 0.045 0.211 1560 Planarity : 0.006 0.094 1680 Dihedral : 6.675 36.270 1319 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.68 % Favored : 89.41 % Rotamer: Outliers : 0.19 % Allowed : 5.56 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % Twisted General : 0.09 % 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: -0.84 (0.24), residues: 1209 helix: 1.34 (0.19), residues: 692 sheet: -2.66 (0.42), residues: 114 loop : -3.44 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 67 HIS 0.008 0.002 HIS C 58 PHE 0.042 0.003 PHE C 162 TYR 0.023 0.002 TYR C 90 ARG 0.005 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.1891 time to fit residues: 53.4336 Evaluate side-chains 126 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0944 time to fit residues: 1.6879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9894 Z= 0.268 Angle : 0.765 10.062 13488 Z= 0.392 Chirality : 0.044 0.206 1560 Planarity : 0.006 0.086 1680 Dihedral : 6.297 33.834 1319 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.02 % Favored : 91.07 % Rotamer: Outliers : 0.19 % Allowed : 3.55 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % 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: -0.74 (0.24), residues: 1209 helix: 1.26 (0.19), residues: 693 sheet: -2.30 (0.46), residues: 107 loop : -3.17 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 404 HIS 0.007 0.001 HIS C 58 PHE 0.037 0.002 PHE C 162 TYR 0.028 0.002 TYR C 90 ARG 0.002 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.1864 time to fit residues: 51.2052 Evaluate side-chains 127 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0987 time to fit residues: 1.6548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9894 Z= 0.224 Angle : 0.730 10.250 13488 Z= 0.370 Chirality : 0.042 0.192 1560 Planarity : 0.005 0.083 1680 Dihedral : 5.963 33.298 1319 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.94 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 1.85 % 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: -0.63 (0.25), residues: 1209 helix: 1.26 (0.20), residues: 698 sheet: -2.04 (0.48), residues: 104 loop : -3.07 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 67 HIS 0.005 0.001 HIS C 58 PHE 0.037 0.002 PHE A 677 TYR 0.021 0.002 TYR C 90 ARG 0.005 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1878 time to fit residues: 51.0216 Evaluate side-chains 133 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 0.0010 chunk 28 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 overall best weight: 1.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9894 Z= 0.209 Angle : 0.757 10.235 13488 Z= 0.380 Chirality : 0.042 0.198 1560 Planarity : 0.005 0.076 1680 Dihedral : 5.757 29.613 1319 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.78 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1209 helix: 1.18 (0.20), residues: 699 sheet: -2.03 (0.48), residues: 109 loop : -3.03 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 244 HIS 0.006 0.001 HIS B 81 PHE 0.026 0.002 PHE A 302 TYR 0.021 0.002 TYR C 90 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2089 time to fit residues: 59.5854 Evaluate side-chains 136 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS A 428 GLN A 449 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9894 Z= 0.330 Angle : 0.798 11.963 13488 Z= 0.412 Chirality : 0.044 0.217 1560 Planarity : 0.006 0.081 1680 Dihedral : 6.016 29.973 1319 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.43 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -0.86 (0.24), residues: 1209 helix: 1.01 (0.19), residues: 686 sheet: -2.15 (0.47), residues: 115 loop : -2.92 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 244 HIS 0.013 0.002 HIS C 171 PHE 0.041 0.002 PHE C 162 TYR 0.025 0.002 TYR A 565 ARG 0.008 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1917 time to fit residues: 47.5540 Evaluate side-chains 114 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 111 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9894 Z= 0.214 Angle : 0.750 9.938 13488 Z= 0.381 Chirality : 0.043 0.220 1560 Planarity : 0.005 0.080 1680 Dihedral : 5.745 28.946 1319 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.11 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % 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: -0.80 (0.25), residues: 1209 helix: 1.01 (0.20), residues: 697 sheet: -1.89 (0.48), residues: 113 loop : -3.00 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 244 HIS 0.009 0.001 HIS C 171 PHE 0.032 0.002 PHE A 181 TYR 0.018 0.002 TYR A 554 ARG 0.007 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1996 time to fit residues: 49.7445 Evaluate side-chains 130 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9894 Z= 0.447 Angle : 0.889 9.527 13488 Z= 0.465 Chirality : 0.046 0.193 1560 Planarity : 0.007 0.088 1680 Dihedral : 6.402 33.235 1319 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 30.20 Ramachandran Plot: Outliers : 0.99 % Allowed : 10.01 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.29 (0.24), residues: 1209 helix: 0.55 (0.19), residues: 683 sheet: -2.14 (0.47), residues: 115 loop : -2.91 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 244 HIS 0.010 0.003 HIS C 58 PHE 0.035 0.003 PHE B 411 TYR 0.024 0.002 TYR C 90 ARG 0.008 0.001 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2009 time to fit residues: 45.2814 Evaluate side-chains 111 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.6911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9894 Z= 0.263 Angle : 0.780 9.647 13488 Z= 0.398 Chirality : 0.045 0.214 1560 Planarity : 0.006 0.081 1680 Dihedral : 6.070 32.391 1319 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.44 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.99 (0.24), residues: 1209 helix: 0.83 (0.20), residues: 685 sheet: -2.10 (0.47), residues: 115 loop : -2.83 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 244 HIS 0.008 0.002 HIS C 171 PHE 0.029 0.002 PHE A 302 TYR 0.023 0.002 TYR A 565 ARG 0.007 0.001 ARG C 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1932 time to fit residues: 44.6586 Evaluate side-chains 124 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 367 GLN A 428 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.050888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043334 restraints weight = 71776.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.044353 restraints weight = 47817.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.045036 restraints weight = 35699.388| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9894 Z= 0.213 Angle : 0.772 10.066 13488 Z= 0.387 Chirality : 0.044 0.219 1560 Planarity : 0.005 0.076 1680 Dihedral : 5.786 30.301 1319 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.68 % Favored : 90.65 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.88 (0.25), residues: 1209 helix: 0.88 (0.20), residues: 695 sheet: -1.98 (0.47), residues: 115 loop : -2.82 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 244 HIS 0.007 0.001 HIS C 171 PHE 0.028 0.002 PHE A 302 TYR 0.029 0.002 TYR C 90 ARG 0.007 0.001 ARG C 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2004.16 seconds wall clock time: 37 minutes 47.85 seconds (2267.85 seconds total)