Starting phenix.real_space_refine on Tue Sep 24 15:35:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/09_2024/7s0e_24788.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/09_2024/7s0e_24788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/09_2024/7s0e_24788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/09_2024/7s0e_24788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/09_2024/7s0e_24788.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0e_24788/09_2024/7s0e_24788.cif" } resolution = 4.9 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= 0.009 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 5234 2.51 5 N 1373 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4918 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 639, 4909 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 34, 'TRANS': 604} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Conformer: "B" Number of residues, atoms: 639, 4909 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 34, 'TRANS': 604} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 bond proxies already assigned to first conformer: 5016 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1673 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "L" Number of atoms: 1657 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1687 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.40 Time building chain proxies: 9.04, per 1000 atoms: 1.10 Number of scatterers: 8248 At special positions: 0 Unit cell: (91.245, 109.494, 171.193, 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 1605 8.00 N 1373 7.00 C 5234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG BCYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 24 sheets defined 7.4% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.930A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.697A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.123A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.843A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.538A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.876A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.696A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 229 removed outlier: 5.395A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 145 removed outlier: 7.707A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.579A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.669A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.669A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.699A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.545A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.821A pdb=" N ASN A 641 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.519A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.837A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 128 through 130 removed outlier: 5.038A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 143 through 144 Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.508A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.928A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AC4, first strand: chain 'L' and resid 129 through 130 Processing sheet with id=AC5, first strand: chain 'L' and resid 133 through 139 removed outlier: 3.890A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.654A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 491 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: 2.59 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2653 1.34 - 1.47: 2219 1.47 - 1.60: 3535 1.60 - 1.73: 0 1.73 - 1.86: 42 Bond restraints: 8449 Sorted by residual: bond pdb=" C THR H 173 " pdb=" N PHE H 174 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.46e-02 4.69e+03 1.29e+01 bond pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta sigma weight residual 1.462 1.497 -0.034 1.06e-02 8.90e+03 1.04e+01 bond pdb=" N ASN L 34 " pdb=" CA ASN L 34 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.18e-02 7.18e+03 1.03e+01 bond pdb=" N GLY H 107 " pdb=" CA GLY H 107 " ideal model delta sigma weight residual 1.438 1.482 -0.044 1.41e-02 5.03e+03 9.54e+00 bond pdb=" N GLN L 89 " pdb=" CA GLN L 89 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.03e+00 ... (remaining 8444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 11265 2.65 - 5.29: 230 5.29 - 7.94: 14 7.94 - 10.58: 4 10.58 - 13.23: 1 Bond angle restraints: 11514 Sorted by residual: angle pdb=" N PRO A 621 " pdb=" CA PRO A 621 " pdb=" CB PRO A 621 " ideal model delta sigma weight residual 103.25 111.20 -7.95 1.05e+00 9.07e-01 5.74e+01 angle pdb=" N PRO A 631 " pdb=" CA PRO A 631 " pdb=" CB PRO A 631 " ideal model delta sigma weight residual 103.25 111.10 -7.85 1.05e+00 9.07e-01 5.58e+01 angle pdb=" C GLU H 156 " pdb=" N PRO H 157 " pdb=" CD PRO H 157 " ideal model delta sigma weight residual 120.60 107.37 13.23 2.20e+00 2.07e-01 3.61e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.10 108.57 4.53 9.70e-01 1.06e+00 2.18e+01 angle pdb=" N TRP H 111 " pdb=" CA TRP H 111 " pdb=" C TRP H 111 " ideal model delta sigma weight residual 110.91 116.38 -5.47 1.17e+00 7.31e-01 2.18e+01 ... (remaining 11509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4585 17.77 - 35.53: 330 35.53 - 53.30: 65 53.30 - 71.06: 18 71.06 - 88.83: 7 Dihedral angle restraints: 5005 sinusoidal: 1874 harmonic: 3131 Sorted by residual: dihedral pdb=" CA ASN H 163 " pdb=" C ASN H 163 " pdb=" N SER H 164 " pdb=" CA SER H 164 " ideal model delta harmonic sigma weight residual 180.00 139.04 40.96 0 5.00e+00 4.00e-02 6.71e+01 dihedral pdb=" CA TRP H 162 " pdb=" C TRP H 162 " pdb=" N ASN H 163 " pdb=" CA ASN H 163 " ideal model delta harmonic sigma weight residual 180.00 144.92 35.08 0 5.00e+00 4.00e-02 4.92e+01 dihedral pdb=" CA SER H 164 " pdb=" C SER H 164 " pdb=" N GLY H 165 " pdb=" CA GLY H 165 " ideal model delta harmonic sigma weight residual 180.00 145.88 34.12 0 5.00e+00 4.00e-02 4.66e+01 ... (remaining 5002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1123 0.078 - 0.155: 153 0.155 - 0.233: 8 0.233 - 0.311: 4 0.311 - 0.389: 2 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CA TYR H 33 " pdb=" N TYR H 33 " pdb=" C TYR H 33 " pdb=" CB TYR H 33 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ILE L 29 " pdb=" N ILE L 29 " pdb=" C ILE L 29 " pdb=" CB ILE L 29 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1287 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " -0.057 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO H 157 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 560 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C LEU A 560 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU A 560 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO A 561 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 271 " -0.042 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO A 272 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " -0.036 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 78 2.49 - 3.09: 6018 3.09 - 3.69: 12982 3.69 - 4.30: 17789 4.30 - 4.90: 28277 Nonbonded interactions: 65144 Sorted by model distance: nonbonded pdb=" CG TYR H 33 " pdb=" OD2 ASP H 99 " model vdw 1.886 3.260 nonbonded pdb=" N GLY H 165 " pdb=" O TYR H 202 " model vdw 1.950 3.120 nonbonded pdb=" N ALA H 166 " pdb=" O THR H 201 " model vdw 2.090 3.120 nonbonded pdb=" OG1 THR H 28 " pdb=" OG SER H 31 " model vdw 2.133 3.040 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.158 3.040 ... (remaining 65139 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=0.04 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: 8.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.150 Find NCS groups from input model: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 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 : 0.004 0.052 8449 Z= 0.272 Angle : 0.868 13.225 11514 Z= 0.524 Chirality : 0.053 0.389 1290 Planarity : 0.006 0.085 1490 Dihedral : 13.436 88.828 2954 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.06 % Favored : 91.27 % Rotamer: Outliers : 1.22 % Allowed : 0.78 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.76 (0.25), residues: 1059 helix: -2.63 (0.67), residues: 49 sheet: -0.61 (0.30), residues: 285 loop : -1.35 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP L 91 HIS 0.004 0.001 HIS H 208 PHE 0.023 0.002 PHE A 329 TYR 0.016 0.002 TYR L 49 ARG 0.006 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 SER cc_start: 0.9061 (m) cc_final: 0.8842 (p) REVERT: A 374 PHE cc_start: 0.7807 (m-10) cc_final: 0.7443 (m-80) REVERT: A 392 PHE cc_start: 0.7798 (m-80) cc_final: 0.7174 (m-80) REVERT: A 418 ILE cc_start: 0.9282 (tt) cc_final: 0.8703 (tp) REVERT: A 455 LEU cc_start: 0.8401 (mm) cc_final: 0.7967 (mm) REVERT: H 5 VAL cc_start: 0.8765 (m) cc_final: 0.8564 (p) REVERT: H 20 LEU cc_start: 0.9397 (mt) cc_final: 0.8035 (mt) REVERT: H 49 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8073 (t) REVERT: H 54 SER cc_start: 0.6827 (OUTLIER) cc_final: 0.6384 (t) REVERT: H 58 THR cc_start: 0.8217 (t) cc_final: 0.7490 (m) REVERT: H 217 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8217 (ptmt) REVERT: L 35 TRP cc_start: 0.8199 (m100) cc_final: 0.7975 (m100) REVERT: L 50 ASP cc_start: 0.8262 (m-30) cc_final: 0.8041 (m-30) REVERT: L 70 ASP cc_start: 0.8978 (p0) cc_final: 0.8589 (p0) REVERT: L 71 PHE cc_start: 0.7069 (m-80) cc_final: 0.6409 (t80) REVERT: L 98 PHE cc_start: 0.7618 (m-80) cc_final: 0.6926 (m-80) REVERT: L 136 LEU cc_start: 0.8689 (mp) cc_final: 0.8452 (mp) outliers start: 11 outliers final: 3 residues processed: 133 average time/residue: 0.1882 time to fit residues: 35.7386 Evaluate side-chains 87 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 196 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 8449 Z= 0.318 Angle : 0.775 12.494 11514 Z= 0.415 Chirality : 0.048 0.226 1290 Planarity : 0.006 0.088 1490 Dihedral : 6.334 39.821 1159 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.44 % Favored : 91.18 % Rotamer: Outliers : 0.22 % Allowed : 3.66 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.98 (0.24), residues: 1059 helix: -2.99 (0.54), residues: 54 sheet: -1.00 (0.28), residues: 302 loop : -1.35 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 353 HIS 0.011 0.002 HIS H 208 PHE 0.023 0.002 PHE A 65 TYR 0.025 0.003 TYR H 33 ARG 0.009 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7809 (m-10) cc_final: 0.7522 (m-80) REVERT: A 392 PHE cc_start: 0.7607 (m-80) cc_final: 0.6542 (m-80) REVERT: H 5 VAL cc_start: 0.8932 (m) cc_final: 0.8730 (p) REVERT: H 36 TRP cc_start: 0.8359 (m100) cc_final: 0.8022 (m100) REVERT: H 79 LEU cc_start: 0.8979 (tp) cc_final: 0.8665 (tp) REVERT: H 158 VAL cc_start: 0.8007 (m) cc_final: 0.7751 (p) REVERT: L 71 PHE cc_start: 0.7528 (m-80) cc_final: 0.7125 (m-80) REVERT: L 72 THR cc_start: 0.8230 (p) cc_final: 0.7929 (t) REVERT: L 175 LEU cc_start: 0.8740 (tp) cc_final: 0.8527 (tp) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.1685 time to fit residues: 26.8112 Evaluate side-chains 68 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 8449 Z= 0.305 Angle : 0.760 13.243 11514 Z= 0.402 Chirality : 0.047 0.212 1290 Planarity : 0.005 0.061 1490 Dihedral : 6.256 37.733 1159 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.92 % Favored : 90.80 % Rotamer: Outliers : 0.22 % Allowed : 2.77 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.08 (0.24), residues: 1059 helix: -3.12 (0.51), residues: 54 sheet: -0.88 (0.29), residues: 299 loop : -1.52 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 353 HIS 0.007 0.002 HIS H 35 PHE 0.031 0.002 PHE H 108 TYR 0.026 0.003 TYR H 33 ARG 0.006 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7561 (m-80) cc_final: 0.6973 (m-80) REVERT: H 5 VAL cc_start: 0.9054 (m) cc_final: 0.8849 (p) REVERT: H 153 TYR cc_start: 0.8173 (p90) cc_final: 0.7729 (p90) REVERT: L 70 ASP cc_start: 0.9048 (p0) cc_final: 0.8744 (p0) REVERT: L 71 PHE cc_start: 0.7714 (m-80) cc_final: 0.7083 (m-10) REVERT: L 137 ASN cc_start: 0.7656 (t0) cc_final: 0.7282 (t0) REVERT: L 175 LEU cc_start: 0.9099 (tp) cc_final: 0.8715 (tp) outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.1810 time to fit residues: 26.5632 Evaluate side-chains 68 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 0.0570 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8449 Z= 0.258 Angle : 0.736 13.945 11514 Z= 0.388 Chirality : 0.046 0.204 1290 Planarity : 0.005 0.071 1490 Dihedral : 6.173 37.163 1159 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.16 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.04 (0.24), residues: 1059 helix: -3.04 (0.53), residues: 56 sheet: -0.86 (0.29), residues: 296 loop : -1.48 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 353 HIS 0.004 0.001 HIS H 172 PHE 0.023 0.002 PHE A 65 TYR 0.020 0.002 TYR H 33 ARG 0.029 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9252 (pt) cc_final: 0.8878 (tp) REVERT: A 353 TRP cc_start: 0.4824 (p-90) cc_final: 0.4189 (p-90) REVERT: A 392 PHE cc_start: 0.7692 (m-80) cc_final: 0.7022 (m-80) REVERT: A 398 ASP cc_start: 0.8360 (m-30) cc_final: 0.8034 (m-30) REVERT: H 153 TYR cc_start: 0.8133 (p90) cc_final: 0.7846 (p90) REVERT: L 71 PHE cc_start: 0.7561 (m-80) cc_final: 0.6718 (m-10) REVERT: L 137 ASN cc_start: 0.7464 (t0) cc_final: 0.7221 (t0) REVERT: L 169 LYS cc_start: 0.9679 (mmmt) cc_final: 0.8911 (tmtt) REVERT: L 175 LEU cc_start: 0.9048 (tp) cc_final: 0.8758 (tp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1636 time to fit residues: 23.2301 Evaluate side-chains 67 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8449 Z= 0.229 Angle : 0.704 15.399 11514 Z= 0.370 Chirality : 0.046 0.188 1290 Planarity : 0.005 0.061 1490 Dihedral : 5.983 37.453 1159 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.54 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.09 (0.24), residues: 1059 helix: -2.92 (0.55), residues: 57 sheet: -0.87 (0.29), residues: 297 loop : -1.54 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 353 HIS 0.004 0.001 HIS H 172 PHE 0.024 0.002 PHE H 108 TYR 0.018 0.002 TYR H 33 ARG 0.008 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8344 (m-80) cc_final: 0.8118 (m-80) REVERT: A 335 LEU cc_start: 0.9194 (pt) cc_final: 0.8849 (tp) REVERT: A 392 PHE cc_start: 0.7658 (m-80) cc_final: 0.6936 (m-80) REVERT: H 153 TYR cc_start: 0.8223 (p90) cc_final: 0.7816 (p90) REVERT: L 70 ASP cc_start: 0.9020 (p0) cc_final: 0.8764 (p0) REVERT: L 71 PHE cc_start: 0.7621 (m-80) cc_final: 0.6762 (m-10) REVERT: L 169 LYS cc_start: 0.9685 (mmmt) cc_final: 0.8985 (tmtt) REVERT: L 175 LEU cc_start: 0.9078 (tp) cc_final: 0.8707 (tp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1605 time to fit residues: 21.5836 Evaluate side-chains 65 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8449 Z= 0.281 Angle : 0.739 15.273 11514 Z= 0.391 Chirality : 0.047 0.176 1290 Planarity : 0.005 0.058 1490 Dihedral : 6.247 37.974 1159 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.68 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -2.14 (0.25), residues: 1059 helix: -2.69 (0.60), residues: 51 sheet: -1.06 (0.28), residues: 316 loop : -1.55 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 353 HIS 0.012 0.002 HIS H 208 PHE 0.029 0.002 PHE H 108 TYR 0.019 0.002 TYR H 33 ARG 0.016 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8453 (m-80) cc_final: 0.8246 (m-80) REVERT: A 392 PHE cc_start: 0.7603 (m-80) cc_final: 0.6773 (m-80) REVERT: H 46 GLU cc_start: 0.8640 (tt0) cc_final: 0.8315 (tt0) REVERT: L 166 GLN cc_start: 0.8005 (mm110) cc_final: 0.7245 (mm-40) REVERT: L 169 LYS cc_start: 0.9724 (mmmt) cc_final: 0.9014 (tmtt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1863 time to fit residues: 23.4239 Evaluate side-chains 63 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 8449 Z= 0.213 Angle : 0.701 15.899 11514 Z= 0.366 Chirality : 0.046 0.174 1290 Planarity : 0.005 0.082 1490 Dihedral : 5.864 34.485 1159 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.16 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.05 (0.25), residues: 1059 helix: -2.75 (0.57), residues: 57 sheet: -0.95 (0.28), residues: 316 loop : -1.47 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 353 HIS 0.007 0.001 HIS H 208 PHE 0.043 0.002 PHE H 108 TYR 0.016 0.002 TYR H 33 ARG 0.009 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9197 (pt) cc_final: 0.8850 (tp) REVERT: A 392 PHE cc_start: 0.7616 (m-80) cc_final: 0.6705 (m-80) REVERT: A 398 ASP cc_start: 0.8486 (m-30) cc_final: 0.8218 (m-30) REVERT: H 46 GLU cc_start: 0.8627 (tt0) cc_final: 0.8365 (tt0) REVERT: H 153 TYR cc_start: 0.7973 (p90) cc_final: 0.7772 (p90) REVERT: H 217 LYS cc_start: 0.8507 (mtpt) cc_final: 0.6944 (mttt) REVERT: L 71 PHE cc_start: 0.7291 (m-80) cc_final: 0.7036 (m-80) REVERT: L 98 PHE cc_start: 0.7267 (m-80) cc_final: 0.6147 (m-80) REVERT: L 136 LEU cc_start: 0.9306 (mp) cc_final: 0.8904 (mp) REVERT: L 169 LYS cc_start: 0.9709 (mmmt) cc_final: 0.8958 (tmtt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1792 time to fit residues: 22.9679 Evaluate side-chains 65 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8449 Z= 0.203 Angle : 0.688 15.545 11514 Z= 0.359 Chirality : 0.046 0.179 1290 Planarity : 0.005 0.078 1490 Dihedral : 5.689 39.617 1159 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.35 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.97 (0.25), residues: 1059 helix: -2.74 (0.52), residues: 58 sheet: -0.89 (0.28), residues: 315 loop : -1.42 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 353 HIS 0.005 0.001 HIS H 208 PHE 0.039 0.002 PHE H 108 TYR 0.016 0.002 TYR H 33 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9174 (pt) cc_final: 0.8845 (tp) REVERT: A 392 PHE cc_start: 0.7611 (m-80) cc_final: 0.6707 (m-80) REVERT: A 398 ASP cc_start: 0.8549 (m-30) cc_final: 0.8227 (m-30) REVERT: A 418 ILE cc_start: 0.9165 (pt) cc_final: 0.8861 (mm) REVERT: H 153 TYR cc_start: 0.8074 (p90) cc_final: 0.7847 (p90) REVERT: L 4 MET cc_start: 0.9171 (mpp) cc_final: 0.8637 (mpp) REVERT: L 98 PHE cc_start: 0.7270 (m-80) cc_final: 0.6260 (m-80) REVERT: L 136 LEU cc_start: 0.9285 (mp) cc_final: 0.8935 (mp) REVERT: L 169 LYS cc_start: 0.9716 (mmmt) cc_final: 0.8961 (tmtt) REVERT: L 185 ASP cc_start: 0.8832 (t0) cc_final: 0.7922 (m-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1873 time to fit residues: 24.3940 Evaluate side-chains 61 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8449 Z= 0.218 Angle : 0.705 15.726 11514 Z= 0.366 Chirality : 0.046 0.178 1290 Planarity : 0.005 0.069 1490 Dihedral : 5.680 37.063 1159 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.92 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.97 (0.25), residues: 1059 helix: -2.48 (0.58), residues: 56 sheet: -0.89 (0.29), residues: 317 loop : -1.45 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 94 HIS 0.006 0.001 HIS H 208 PHE 0.050 0.002 PHE A 65 TYR 0.013 0.002 TYR H 33 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9186 (pt) cc_final: 0.8864 (tp) REVERT: A 392 PHE cc_start: 0.7607 (m-80) cc_final: 0.6797 (m-80) REVERT: A 398 ASP cc_start: 0.8594 (m-30) cc_final: 0.8253 (m-30) REVERT: A 418 ILE cc_start: 0.9176 (pt) cc_final: 0.8901 (mm) REVERT: H 36 TRP cc_start: 0.8489 (m100) cc_final: 0.8225 (m100) REVERT: H 153 TYR cc_start: 0.8154 (p90) cc_final: 0.7812 (p90) REVERT: L 4 MET cc_start: 0.9098 (mpp) cc_final: 0.8667 (mpp) REVERT: L 98 PHE cc_start: 0.7284 (m-80) cc_final: 0.6220 (m-80) REVERT: L 136 LEU cc_start: 0.9291 (mp) cc_final: 0.8973 (mp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1802 time to fit residues: 22.5404 Evaluate side-chains 62 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0470 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 64 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN L 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8449 Z= 0.188 Angle : 0.694 16.041 11514 Z= 0.359 Chirality : 0.046 0.181 1290 Planarity : 0.005 0.071 1490 Dihedral : 5.515 35.770 1159 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.16 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.86 (0.25), residues: 1059 helix: -2.39 (0.58), residues: 56 sheet: -0.76 (0.29), residues: 315 loop : -1.40 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP L 94 HIS 0.004 0.001 HIS H 208 PHE 0.037 0.002 PHE A 65 TYR 0.015 0.001 TYR H 33 ARG 0.005 0.001 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9189 (pt) cc_final: 0.8862 (tp) REVERT: A 392 PHE cc_start: 0.7578 (m-80) cc_final: 0.6732 (m-80) REVERT: A 398 ASP cc_start: 0.8558 (m-30) cc_final: 0.8194 (m-30) REVERT: A 418 ILE cc_start: 0.9155 (pt) cc_final: 0.8905 (mm) REVERT: H 153 TYR cc_start: 0.7997 (p90) cc_final: 0.7759 (p90) REVERT: L 4 MET cc_start: 0.9023 (mpp) cc_final: 0.8560 (mpp) REVERT: L 47 LEU cc_start: 0.8305 (mp) cc_final: 0.7955 (mp) REVERT: L 98 PHE cc_start: 0.7245 (m-80) cc_final: 0.6300 (m-80) REVERT: L 136 LEU cc_start: 0.9239 (mp) cc_final: 0.8924 (mp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1805 time to fit residues: 23.6534 Evaluate side-chains 59 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 0.0670 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** 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 = 0.3631 r_free = 0.3631 target = 0.072746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055090 restraints weight = 135115.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057851 restraints weight = 74705.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059793 restraints weight = 48758.995| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8449 Z= 0.195 Angle : 0.683 15.795 11514 Z= 0.355 Chirality : 0.046 0.185 1290 Planarity : 0.005 0.065 1490 Dihedral : 5.525 34.805 1159 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.25 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.71 (0.25), residues: 1059 helix: -2.35 (0.58), residues: 56 sheet: -0.46 (0.30), residues: 302 loop : -1.39 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 94 HIS 0.006 0.001 HIS H 208 PHE 0.035 0.002 PHE A 65 TYR 0.012 0.001 TYR L 32 ARG 0.004 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.61 seconds wall clock time: 37 minutes 54.82 seconds (2274.82 seconds total)