Starting phenix.real_space_refine on Wed Feb 12 21:29:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0e_24788/02_2025/7s0e_24788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0e_24788/02_2025/7s0e_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/cci-nas-00/data/ceres_data/7s0e_24788/02_2025/7s0e_24788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0e_24788/02_2025/7s0e_24788.map" model { file = "/net/cci-nas-00/data/ceres_data/7s0e_24788/02_2025/7s0e_24788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0e_24788/02_2025/7s0e_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.83, per 1000 atoms: 0.59 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: 1.85 Conformation dependent library (CDL) restraints added in 1.7 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: 1.15 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: 2.49 Time building geometry restraints manager: 2.22 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: 11.970 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: 7.520 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.889 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: 0.1819 time to fit residues: 34.8325 Evaluate side-chains 87 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.073184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055277 restraints weight = 132691.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058881 restraints weight = 70796.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.060799 restraints weight = 42419.103| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 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 : 21.55 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 to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8592 (m-80) cc_final: 0.8376 (m-80) REVERT: A 374 PHE cc_start: 0.7831 (m-10) cc_final: 0.7559 (m-80) REVERT: A 392 PHE cc_start: 0.7684 (m-80) cc_final: 0.6626 (m-80) REVERT: H 36 TRP cc_start: 0.8420 (m100) cc_final: 0.8073 (m100) REVERT: H 79 LEU cc_start: 0.9080 (tp) cc_final: 0.8701 (tp) REVERT: H 158 VAL cc_start: 0.8098 (m) cc_final: 0.7842 (p) REVERT: L 71 PHE cc_start: 0.7452 (m-80) cc_final: 0.6998 (m-80) REVERT: L 72 THR cc_start: 0.8227 (p) cc_final: 0.7980 (t) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.1666 time to fit residues: 26.4839 Evaluate side-chains 69 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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 166 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 = 0.3640 r_free = 0.3640 target = 0.073450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056339 restraints weight = 110503.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.058784 restraints weight = 65518.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.060503 restraints weight = 44777.419| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8449 Z= 0.250 Angle : 0.711 13.534 11514 Z= 0.376 Chirality : 0.046 0.207 1290 Planarity : 0.005 0.053 1490 Dihedral : 5.954 37.710 1159 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.16 % Favored : 91.56 % Rotamer: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % 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: -2.02 (0.24), residues: 1059 helix: -3.01 (0.53), residues: 54 sheet: -0.96 (0.29), residues: 282 loop : -1.41 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 353 HIS 0.004 0.001 HIS H 208 PHE 0.027 0.002 PHE H 108 TYR 0.027 0.002 TYR H 33 ARG 0.005 0.001 ARG A 457 *********************** 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 108 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9294 (pt) cc_final: 0.8962 (tp) REVERT: A 392 PHE cc_start: 0.7661 (m-80) cc_final: 0.7117 (m-80) REVERT: H 46 GLU cc_start: 0.8793 (tt0) cc_final: 0.8577 (tt0) REVERT: H 158 VAL cc_start: 0.8137 (m) cc_final: 0.7806 (p) REVERT: H 217 LYS cc_start: 0.7778 (mttt) cc_final: 0.7526 (ptpp) REVERT: L 70 ASP cc_start: 0.8943 (p0) cc_final: 0.8698 (p0) REVERT: L 71 PHE cc_start: 0.7212 (m-80) cc_final: 0.6806 (m-80) REVERT: L 94 TRP cc_start: 0.7242 (t-100) cc_final: 0.6644 (t60) REVERT: L 137 ASN cc_start: 0.7723 (t0) cc_final: 0.7417 (t0) REVERT: L 175 LEU cc_start: 0.9037 (tp) cc_final: 0.8588 (tp) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1845 time to fit residues: 28.6454 Evaluate side-chains 74 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 43 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 97 optimal weight: 0.2980 overall best weight: 1.4502 ------------------------------------------------------------------------------- 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 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.072664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053831 restraints weight = 149137.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.056758 restraints weight = 77032.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058834 restraints weight = 49419.253| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 8449 Z= 0.263 Angle : 0.736 13.562 11514 Z= 0.391 Chirality : 0.046 0.191 1290 Planarity : 0.007 0.160 1490 Dihedral : 6.089 38.171 1159 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.63 % Favored : 91.08 % Rotamer: Outliers : 0.11 % Allowed : 2.11 % Favored : 97.78 % 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 (0.24), residues: 1059 helix: -3.01 (0.52), residues: 56 sheet: -0.89 (0.29), residues: 302 loop : -1.39 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 353 HIS 0.007 0.001 HIS H 35 PHE 0.033 0.002 PHE H 108 TYR 0.021 0.002 TYR H 33 ARG 0.039 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 92 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7708 (m-80) cc_final: 0.7141 (m-80) REVERT: H 158 VAL cc_start: 0.8326 (m) cc_final: 0.8019 (p) REVERT: H 214 LYS cc_start: 0.9044 (tptp) cc_final: 0.8611 (mptt) REVERT: H 216 ASP cc_start: 0.6992 (m-30) cc_final: 0.6658 (m-30) REVERT: L 48 ILE cc_start: 0.9195 (mt) cc_final: 0.8877 (tt) REVERT: L 71 PHE cc_start: 0.7301 (m-80) cc_final: 0.6616 (m-10) REVERT: L 94 TRP cc_start: 0.7322 (t-100) cc_final: 0.6675 (t60) REVERT: L 135 LEU cc_start: 0.8133 (tp) cc_final: 0.7928 (tt) REVERT: L 169 LYS cc_start: 0.9695 (mmmt) cc_final: 0.8924 (tmtt) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.1679 time to fit residues: 23.3532 Evaluate side-chains 69 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.068855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.052547 restraints weight = 109970.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.054721 restraints weight = 66886.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.056308 restraints weight = 46191.316| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 8449 Z= 0.365 Angle : 0.829 14.743 11514 Z= 0.440 Chirality : 0.048 0.185 1290 Planarity : 0.007 0.143 1490 Dihedral : 6.766 42.590 1159 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.77 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -2.24 (0.24), residues: 1059 helix: -3.04 (0.54), residues: 50 sheet: -1.06 (0.29), residues: 291 loop : -1.63 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 353 HIS 0.010 0.002 HIS H 102 PHE 0.032 0.003 PHE H 108 TYR 0.025 0.003 TYR A 505 ARG 0.036 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 88 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7598 (m-80) cc_final: 0.6783 (m-80) REVERT: H 46 GLU cc_start: 0.8876 (tt0) cc_final: 0.8652 (tt0) REVERT: H 153 TYR cc_start: 0.8324 (p90) cc_final: 0.7849 (p90) REVERT: L 48 ILE cc_start: 0.9238 (mt) cc_final: 0.9013 (mm) REVERT: L 71 PHE cc_start: 0.7692 (m-80) cc_final: 0.7023 (m-10) REVERT: L 175 LEU cc_start: 0.9273 (tp) cc_final: 0.8995 (tp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2004 time to fit residues: 25.6442 Evaluate side-chains 62 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 0.0010 chunk 64 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.073115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.055507 restraints weight = 119831.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058129 restraints weight = 70027.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.059978 restraints weight = 47190.095| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8449 Z= 0.199 Angle : 0.707 15.841 11514 Z= 0.370 Chirality : 0.047 0.172 1290 Planarity : 0.005 0.072 1490 Dihedral : 5.919 37.625 1159 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.59 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -2.03 (0.25), residues: 1059 helix: -2.88 (0.54), residues: 56 sheet: -0.93 (0.28), residues: 308 loop : -1.45 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 353 HIS 0.011 0.002 HIS H 208 PHE 0.024 0.002 PHE A 275 TYR 0.018 0.002 TYR L 173 ARG 0.027 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 100 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9239 (pt) cc_final: 0.8893 (tp) REVERT: A 392 PHE cc_start: 0.7725 (m-80) cc_final: 0.6935 (m-80) REVERT: A 396 TYR cc_start: 0.8821 (m-10) cc_final: 0.8439 (m-10) REVERT: H 46 GLU cc_start: 0.8560 (tt0) cc_final: 0.8311 (tt0) REVERT: H 217 LYS cc_start: 0.8469 (mttt) cc_final: 0.7973 (mttt) REVERT: H 218 LYS cc_start: 0.8461 (mttt) cc_final: 0.8158 (mmtt) REVERT: L 4 MET cc_start: 0.9067 (mpp) cc_final: 0.8756 (mpp) REVERT: L 94 TRP cc_start: 0.7672 (t-100) cc_final: 0.6980 (t60) REVERT: L 114 SER cc_start: 0.8393 (t) cc_final: 0.8178 (m) REVERT: L 137 ASN cc_start: 0.8061 (t0) cc_final: 0.7829 (t0) REVERT: L 169 LYS cc_start: 0.9667 (mmmt) cc_final: 0.8866 (tmtt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2063 time to fit residues: 28.8172 Evaluate side-chains 67 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 0.0670 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056328 restraints weight = 106141.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.058756 restraints weight = 64531.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.060490 restraints weight = 44403.746| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8449 Z= 0.187 Angle : 0.688 15.872 11514 Z= 0.357 Chirality : 0.046 0.182 1290 Planarity : 0.005 0.081 1490 Dihedral : 5.642 36.312 1159 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.06 % Favored : 91.65 % 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: -1.93 (0.25), residues: 1059 helix: -2.85 (0.53), residues: 56 sheet: -0.93 (0.28), residues: 321 loop : -1.34 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 353 HIS 0.007 0.001 HIS H 35 PHE 0.020 0.002 PHE A 275 TYR 0.014 0.002 TYR L 32 ARG 0.018 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 92 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8190 (m-80) cc_final: 0.7955 (m-80) REVERT: A 335 LEU cc_start: 0.9244 (pt) cc_final: 0.8947 (tp) REVERT: A 392 PHE cc_start: 0.7672 (m-80) cc_final: 0.6891 (m-80) REVERT: A 396 TYR cc_start: 0.8860 (m-10) cc_final: 0.8480 (m-10) REVERT: A 398 ASP cc_start: 0.8512 (m-30) cc_final: 0.8288 (m-30) REVERT: H 46 GLU cc_start: 0.8565 (tt0) cc_final: 0.8279 (tt0) REVERT: H 217 LYS cc_start: 0.8446 (mttt) cc_final: 0.7976 (mttt) REVERT: H 218 LYS cc_start: 0.8484 (mttt) cc_final: 0.8226 (mmtt) REVERT: L 4 MET cc_start: 0.9088 (mpp) cc_final: 0.8804 (mpp) REVERT: L 71 PHE cc_start: 0.7062 (m-80) cc_final: 0.6763 (m-80) REVERT: L 94 TRP cc_start: 0.7717 (t-100) cc_final: 0.7071 (t60) REVERT: L 114 SER cc_start: 0.8082 (t) cc_final: 0.7873 (m) REVERT: L 137 ASN cc_start: 0.7761 (t0) cc_final: 0.7528 (t0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2046 time to fit residues: 28.1538 Evaluate side-chains 68 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.055738 restraints weight = 121700.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058375 restraints weight = 71970.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.060247 restraints weight = 48760.569| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8449 Z= 0.194 Angle : 0.680 15.868 11514 Z= 0.355 Chirality : 0.046 0.196 1290 Planarity : 0.006 0.103 1490 Dihedral : 5.524 33.556 1159 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.06 % Favored : 91.65 % 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: -1.89 (0.25), residues: 1059 helix: -2.74 (0.54), residues: 57 sheet: -0.81 (0.29), residues: 317 loop : -1.37 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 353 HIS 0.006 0.001 HIS H 208 PHE 0.018 0.002 PHE A 275 TYR 0.015 0.002 TYR H 33 ARG 0.021 0.001 ARG H 98 *********************** 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 92 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9225 (pt) cc_final: 0.8926 (tp) REVERT: A 392 PHE cc_start: 0.7650 (m-80) cc_final: 0.6866 (m-80) REVERT: A 396 TYR cc_start: 0.8863 (m-10) cc_final: 0.8490 (m-10) REVERT: A 398 ASP cc_start: 0.8583 (m-30) cc_final: 0.8247 (m-30) REVERT: A 418 ILE cc_start: 0.9262 (pt) cc_final: 0.9000 (mm) REVERT: H 46 GLU cc_start: 0.8700 (tt0) cc_final: 0.8227 (tt0) REVERT: H 217 LYS cc_start: 0.8442 (mttt) cc_final: 0.7901 (mtpt) REVERT: H 218 LYS cc_start: 0.8552 (mttt) cc_final: 0.8293 (mmtt) REVERT: L 4 MET cc_start: 0.9111 (mpp) cc_final: 0.8813 (mpp) REVERT: L 71 PHE cc_start: 0.7026 (m-80) cc_final: 0.6749 (m-80) REVERT: L 114 SER cc_start: 0.8159 (t) cc_final: 0.7915 (m) REVERT: L 137 ASN cc_start: 0.7839 (t0) cc_final: 0.7510 (t0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1891 time to fit residues: 25.3395 Evaluate side-chains 62 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 37 optimal weight: 0.0030 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.072948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.055858 restraints weight = 108249.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058356 restraints weight = 65095.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060115 restraints weight = 44495.923| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8449 Z= 0.206 Angle : 0.677 14.766 11514 Z= 0.355 Chirality : 0.046 0.196 1290 Planarity : 0.005 0.102 1490 Dihedral : 5.445 37.497 1159 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.11 % Favored : 90.70 % 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: -1.86 (0.25), residues: 1059 helix: -2.70 (0.55), residues: 58 sheet: -0.74 (0.29), residues: 313 loop : -1.37 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 162 HIS 0.006 0.001 HIS H 208 PHE 0.023 0.002 PHE H 108 TYR 0.011 0.002 TYR L 173 ARG 0.021 0.001 ARG H 98 *********************** 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 to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9231 (pt) cc_final: 0.8924 (tp) REVERT: A 392 PHE cc_start: 0.7650 (m-80) cc_final: 0.6886 (m-80) REVERT: A 396 TYR cc_start: 0.8871 (m-10) cc_final: 0.8501 (m-10) REVERT: A 398 ASP cc_start: 0.8652 (m-30) cc_final: 0.8307 (m-30) REVERT: A 418 ILE cc_start: 0.9235 (pt) cc_final: 0.9013 (mm) REVERT: H 46 GLU cc_start: 0.8723 (tt0) cc_final: 0.8354 (tt0) REVERT: H 158 VAL cc_start: 0.8474 (m) cc_final: 0.8194 (p) REVERT: H 217 LYS cc_start: 0.7908 (mttt) cc_final: 0.7225 (ptmt) REVERT: H 218 LYS cc_start: 0.8530 (mttt) cc_final: 0.8208 (mmtt) REVERT: L 4 MET cc_start: 0.9173 (mpp) cc_final: 0.8879 (mpp) REVERT: L 29 ILE cc_start: 0.8852 (mm) cc_final: 0.8581 (mp) REVERT: L 114 SER cc_start: 0.8281 (t) cc_final: 0.8051 (m) REVERT: L 137 ASN cc_start: 0.7744 (t0) cc_final: 0.7407 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1698 time to fit residues: 21.8434 Evaluate side-chains 61 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 9.9990 chunk 105 optimal weight: 0.0470 chunk 85 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- 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** A 641 ASN L 27 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.071525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054221 restraints weight = 120775.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056814 restraints weight = 69834.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058640 restraints weight = 46675.716| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8449 Z= 0.250 Angle : 0.725 14.647 11514 Z= 0.379 Chirality : 0.046 0.219 1290 Planarity : 0.006 0.122 1490 Dihedral : 5.684 41.133 1159 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.39 % Favored : 90.42 % 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: -2.04 (0.25), residues: 1059 helix: -2.67 (0.55), residues: 58 sheet: -0.93 (0.29), residues: 324 loop : -1.48 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP L 35 HIS 0.008 0.002 HIS H 208 PHE 0.054 0.002 PHE A 65 TYR 0.018 0.002 TYR A 28 ARG 0.022 0.001 ARG H 98 ********************** 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 83 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9232 (pt) cc_final: 0.8919 (tp) REVERT: A 392 PHE cc_start: 0.7705 (m-80) cc_final: 0.7062 (m-80) REVERT: A 398 ASP cc_start: 0.8806 (m-30) cc_final: 0.8452 (m-30) REVERT: H 46 GLU cc_start: 0.8870 (tt0) cc_final: 0.8368 (tt0) REVERT: H 217 LYS cc_start: 0.8266 (mttt) cc_final: 0.7722 (mtpt) REVERT: H 218 LYS cc_start: 0.8598 (mttt) cc_final: 0.8308 (mmtt) REVERT: L 4 MET cc_start: 0.9214 (mpp) cc_final: 0.8958 (mpp) REVERT: L 29 ILE cc_start: 0.8953 (mm) cc_final: 0.8710 (mp) REVERT: L 53 ASN cc_start: 0.8578 (t0) cc_final: 0.8232 (t0) REVERT: L 114 SER cc_start: 0.8264 (t) cc_final: 0.8028 (m) REVERT: L 137 ASN cc_start: 0.7755 (t0) cc_final: 0.7362 (t0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1707 time to fit residues: 21.6136 Evaluate side-chains 60 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** L 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.072471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053554 restraints weight = 156532.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.056534 restraints weight = 83824.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058672 restraints weight = 53979.484| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5626 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= 0.208 Angle : 0.704 14.900 11514 Z= 0.367 Chirality : 0.046 0.197 1290 Planarity : 0.006 0.124 1490 Dihedral : 5.532 39.018 1159 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.01 % Favored : 90.80 % 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: -1.99 (0.25), residues: 1059 helix: -2.67 (0.54), residues: 58 sheet: -0.81 (0.29), residues: 317 loop : -1.49 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 36 HIS 0.007 0.001 HIS H 208 PHE 0.041 0.002 PHE A 65 TYR 0.017 0.002 TYR H 33 ARG 0.027 0.001 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.90 seconds wall clock time: 59 minutes 26.91 seconds (3566.91 seconds total)