Starting phenix.real_space_refine on Wed Mar 12 22:36:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0e_24788/03_2025/7s0e_24788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0e_24788/03_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_24788/03_2025/7s0e_24788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0e_24788/03_2025/7s0e_24788.map" model { file = "/net/cci-nas-00/data/ceres_data/7s0e_24788/03_2025/7s0e_24788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0e_24788/03_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-5624/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: 10.28, per 1000 atoms: 1.25 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: 2.12 Conformation dependent library (CDL) restraints added in 1.8 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: 2.58 Time building geometry restraints manager: 2.51 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 29.340 Find NCS groups from input model: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- 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 : 0.910 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: 0.1761 time to fit residues: 33.7145 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 : 0.904 ------------------------------------------------------------------------------- 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 = 0.073183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055278 restraints weight = 132692.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058889 restraints weight = 70816.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.060802 restraints weight = 42237.560| |-----------------------------------------------------------------------------| 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 39.822 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 : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8593 (m-80) cc_final: 0.8376 (m-80) REVERT: A 374 PHE cc_start: 0.7831 (m-10) cc_final: 0.7558 (m-80) REVERT: A 392 PHE cc_start: 0.7685 (m-80) cc_final: 0.6625 (m-80) REVERT: H 36 TRP cc_start: 0.8422 (m100) cc_final: 0.8076 (m100) REVERT: H 79 LEU cc_start: 0.9080 (tp) cc_final: 0.8702 (tp) REVERT: H 158 VAL cc_start: 0.8099 (m) cc_final: 0.7843 (p) REVERT: L 71 PHE cc_start: 0.7451 (m-80) cc_final: 0.6997 (m-80) REVERT: L 72 THR cc_start: 0.8227 (p) cc_final: 0.7981 (t) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.1723 time to fit residues: 27.3920 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 : 0.904 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ** 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 = 0.3634 r_free = 0.3634 target = 0.073182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056199 restraints weight = 110348.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.058620 restraints weight = 65516.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.060321 restraints weight = 44766.601| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 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 = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8449 Z= 0.271 Angle : 0.727 13.465 11514 Z= 0.385 Chirality : 0.046 0.208 1290 Planarity : 0.005 0.053 1490 Dihedral : 6.093 39.003 1159 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.35 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: -2.07 (0.24), residues: 1059 helix: -3.02 (0.53), residues: 54 sheet: -1.08 (0.28), residues: 294 loop : -1.41 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 353 HIS 0.010 0.002 HIS H 35 PHE 0.027 0.002 PHE A 275 TYR 0.018 0.002 TYR H 33 ARG 0.005 0.001 ARG L 61 *********************** 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 106 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7703 (m-80) cc_final: 0.7168 (m-80) REVERT: H 79 LEU cc_start: 0.9055 (tp) cc_final: 0.8802 (tp) REVERT: H 158 VAL cc_start: 0.8187 (m) cc_final: 0.7872 (p) REVERT: H 217 LYS cc_start: 0.8025 (mttt) cc_final: 0.7674 (ptmt) REVERT: L 70 ASP cc_start: 0.8915 (p0) cc_final: 0.8672 (p0) REVERT: L 71 PHE cc_start: 0.6982 (m-80) cc_final: 0.6699 (m-80) REVERT: L 94 TRP cc_start: 0.7172 (t-100) cc_final: 0.6630 (t60) REVERT: L 137 ASN cc_start: 0.7729 (t0) cc_final: 0.7404 (t0) REVERT: L 175 LEU cc_start: 0.8964 (tp) cc_final: 0.8436 (tp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1843 time to fit residues: 28.2700 Evaluate side-chains 69 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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: 0.9980 chunk 82 optimal weight: 0.0030 chunk 43 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 ** 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 = 0.3674 r_free = 0.3674 target = 0.074951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.057667 restraints weight = 152532.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.060983 restraints weight = 76894.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062703 restraints weight = 46834.030| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8449 Z= 0.197 Angle : 0.693 14.245 11514 Z= 0.363 Chirality : 0.047 0.210 1290 Planarity : 0.005 0.069 1490 Dihedral : 5.684 36.990 1159 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.59 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.86 (0.56), residues: 54 sheet: -1.06 (0.26), residues: 347 loop : -1.39 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 353 HIS 0.006 0.001 HIS H 35 PHE 0.021 0.002 PHE H 108 TYR 0.022 0.002 TYR H 33 ARG 0.005 0.001 ARG A 328 *********************** 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 to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9296 (pt) cc_final: 0.8955 (tp) REVERT: A 392 PHE cc_start: 0.7692 (m-80) cc_final: 0.6763 (m-80) REVERT: H 158 VAL cc_start: 0.8077 (m) cc_final: 0.7704 (p) REVERT: L 53 ASN cc_start: 0.8358 (t0) cc_final: 0.8131 (t0) REVERT: L 70 ASP cc_start: 0.8901 (p0) cc_final: 0.8673 (p0) REVERT: L 71 PHE cc_start: 0.7075 (m-80) cc_final: 0.6402 (m-10) REVERT: L 94 TRP cc_start: 0.7123 (t-100) cc_final: 0.6553 (t60) REVERT: L 135 LEU cc_start: 0.7854 (tp) cc_final: 0.7646 (tt) REVERT: L 175 LEU cc_start: 0.8992 (tp) cc_final: 0.8678 (tp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1867 time to fit residues: 26.7206 Evaluate side-chains 70 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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: 0.8980 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** ** L 160 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 = 0.3556 r_free = 0.3556 target = 0.069900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053172 restraints weight = 107221.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.055444 restraints weight = 64661.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057083 restraints weight = 44662.604| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 8449 Z= 0.344 Angle : 0.788 13.903 11514 Z= 0.417 Chirality : 0.047 0.200 1290 Planarity : 0.005 0.066 1490 Dihedral : 6.333 35.669 1159 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.49 % Favored : 90.13 % 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 : 0.30 % 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: -2.17 (0.24), residues: 1059 helix: -3.04 (0.54), residues: 56 sheet: -1.11 (0.28), residues: 312 loop : -1.49 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 353 HIS 0.007 0.002 HIS H 102 PHE 0.034 0.003 PHE H 108 TYR 0.023 0.003 TYR A 28 ARG 0.007 0.001 ARG L 211 *********************** 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 86 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7628 (m-80) cc_final: 0.6885 (m-80) REVERT: H 153 TYR cc_start: 0.8343 (p90) cc_final: 0.7882 (p90) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3163 time to fit residues: 41.6787 Evaluate side-chains 59 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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: 5.9990 chunk 64 optimal weight: 0.0770 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 chunk 15 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 149 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.073749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056133 restraints weight = 119827.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058806 restraints weight = 69626.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.060681 restraints weight = 46689.871| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 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 = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8449 Z= 0.188 Angle : 0.705 15.375 11514 Z= 0.365 Chirality : 0.046 0.173 1290 Planarity : 0.005 0.052 1490 Dihedral : 5.690 32.993 1159 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.50 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -2.06 (0.25), residues: 1059 helix: -2.78 (0.57), residues: 56 sheet: -1.02 (0.28), residues: 315 loop : -1.44 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 111 HIS 0.003 0.001 HIS H 102 PHE 0.027 0.002 PHE H 108 TYR 0.031 0.002 TYR H 33 ARG 0.004 0.001 ARG L 211 *********************** 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 94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9264 (pt) cc_final: 0.8920 (tp) REVERT: A 392 PHE cc_start: 0.7683 (m-80) cc_final: 0.6907 (m-80) REVERT: A 396 TYR cc_start: 0.8851 (m-10) cc_final: 0.8435 (m-10) REVERT: H 46 GLU cc_start: 0.8648 (tt0) cc_final: 0.8314 (tt0) REVERT: H 153 TYR cc_start: 0.8014 (p90) cc_final: 0.7793 (p90) REVERT: H 217 LYS cc_start: 0.7828 (mttt) cc_final: 0.7181 (mttt) REVERT: H 218 LYS cc_start: 0.8732 (mttt) cc_final: 0.8381 (mmtt) REVERT: L 4 MET cc_start: 0.9095 (mpp) cc_final: 0.8740 (mpp) REVERT: L 48 ILE cc_start: 0.9215 (mt) cc_final: 0.8902 (tt) REVERT: L 94 TRP cc_start: 0.7697 (t-100) cc_final: 0.6994 (t60) REVERT: L 114 SER cc_start: 0.8205 (t) cc_final: 0.7992 (m) REVERT: L 169 LYS cc_start: 0.9648 (mmmt) cc_final: 0.8855 (tmtt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2734 time to fit residues: 35.8203 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 : 1.134 ------------------------------------------------------------------------------- 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: 0.4980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.0370 chunk 103 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.074487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057278 restraints weight = 106268.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059807 restraints weight = 63406.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.061605 restraints weight = 43282.182| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8449 Z= 0.176 Angle : 0.682 15.462 11514 Z= 0.352 Chirality : 0.046 0.182 1290 Planarity : 0.005 0.081 1490 Dihedral : 5.402 34.433 1159 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.78 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.99 (0.25), residues: 1059 helix: -2.78 (0.53), residues: 57 sheet: -1.09 (0.27), residues: 331 loop : -1.31 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.002 0.001 HIS A 245 PHE 0.030 0.002 PHE H 108 TYR 0.011 0.001 TYR A 453 ARG 0.006 0.001 ARG L 61 *********************** 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 98 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8161 (m-80) cc_final: 0.7937 (m-80) REVERT: A 335 LEU cc_start: 0.9275 (pt) cc_final: 0.8944 (tp) REVERT: A 392 PHE cc_start: 0.7614 (m-80) cc_final: 0.6779 (m-80) REVERT: A 396 TYR cc_start: 0.8834 (m-10) cc_final: 0.8416 (m-10) REVERT: A 418 ILE cc_start: 0.9230 (pt) cc_final: 0.8942 (mm) REVERT: H 217 LYS cc_start: 0.7763 (mttt) cc_final: 0.7196 (mttt) REVERT: H 218 LYS cc_start: 0.8861 (mttt) cc_final: 0.8584 (mmtt) REVERT: L 4 MET cc_start: 0.9100 (mpp) cc_final: 0.8708 (mpp) REVERT: L 48 ILE cc_start: 0.9136 (mt) cc_final: 0.8824 (tt) REVERT: L 94 TRP cc_start: 0.7696 (t-100) cc_final: 0.7018 (t60) REVERT: L 114 SER cc_start: 0.8140 (t) cc_final: 0.7815 (m) REVERT: L 137 ASN cc_start: 0.7863 (t0) cc_final: 0.7649 (t0) REVERT: L 169 LYS cc_start: 0.9688 (mmmt) cc_final: 0.8923 (tmtt) REVERT: L 175 LEU cc_start: 0.9188 (tp) cc_final: 0.8952 (tp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1962 time to fit residues: 28.0283 Evaluate side-chains 66 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 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: 0.6980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** 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 = 0.3597 r_free = 0.3597 target = 0.071392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.053676 restraints weight = 121200.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056307 restraints weight = 68904.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058164 restraints weight = 45764.565| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8449 Z= 0.244 Angle : 0.729 14.821 11514 Z= 0.380 Chirality : 0.046 0.196 1290 Planarity : 0.005 0.073 1490 Dihedral : 5.790 36.078 1159 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.01 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -2.04 (0.25), residues: 1059 helix: -2.68 (0.55), residues: 57 sheet: -1.06 (0.29), residues: 319 loop : -1.41 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 36 HIS 0.004 0.001 HIS H 172 PHE 0.029 0.002 PHE H 108 TYR 0.018 0.002 TYR H 33 ARG 0.007 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 86 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6073 (mtp) cc_final: 0.5867 (mtp) REVERT: A 335 LEU cc_start: 0.9236 (pt) cc_final: 0.8934 (tp) REVERT: A 392 PHE cc_start: 0.7605 (m-80) cc_final: 0.6886 (m-80) REVERT: A 418 ILE cc_start: 0.9225 (pt) cc_final: 0.8998 (mm) REVERT: H 46 GLU cc_start: 0.8797 (tt0) cc_final: 0.8584 (tt0) REVERT: H 153 TYR cc_start: 0.8227 (p90) cc_final: 0.7851 (p90) REVERT: H 217 LYS cc_start: 0.8034 (mttt) cc_final: 0.7416 (mttt) REVERT: H 218 LYS cc_start: 0.8969 (mttt) cc_final: 0.8605 (mmtt) REVERT: L 4 MET cc_start: 0.9170 (mpp) cc_final: 0.8657 (mpp) REVERT: L 29 ILE cc_start: 0.9276 (mm) cc_final: 0.9055 (mp) REVERT: L 114 SER cc_start: 0.8305 (t) cc_final: 0.8050 (m) REVERT: L 137 ASN cc_start: 0.7807 (t0) cc_final: 0.7577 (t0) REVERT: L 169 LYS cc_start: 0.9732 (mmmt) cc_final: 0.8981 (tmtt) REVERT: L 175 LEU cc_start: 0.9318 (tp) cc_final: 0.9103 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1714 time to fit residues: 21.9782 Evaluate side-chains 59 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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: 5.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.072963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.055741 restraints weight = 108254.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058211 restraints weight = 65275.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.059975 restraints weight = 44797.710| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8449 Z= 0.194 Angle : 0.688 15.018 11514 Z= 0.359 Chirality : 0.046 0.184 1290 Planarity : 0.005 0.061 1490 Dihedral : 5.534 38.700 1159 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.97 % Favored : 91.84 % 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: -1.96 (0.25), residues: 1059 helix: -2.70 (0.53), residues: 58 sheet: -0.89 (0.29), residues: 311 loop : -1.41 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.003 0.001 HIS H 102 PHE 0.026 0.002 PHE H 108 TYR 0.015 0.001 TYR H 33 ARG 0.007 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 90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9199 (pt) cc_final: 0.8896 (tp) REVERT: A 392 PHE cc_start: 0.7638 (m-80) cc_final: 0.6911 (m-80) REVERT: A 396 TYR cc_start: 0.9097 (m-10) cc_final: 0.8734 (m-10) REVERT: A 418 ILE cc_start: 0.9194 (pt) cc_final: 0.8962 (mm) REVERT: H 36 TRP cc_start: 0.8264 (m100) cc_final: 0.6475 (m100) REVERT: H 46 GLU cc_start: 0.8714 (tt0) cc_final: 0.8488 (tt0) REVERT: H 153 TYR cc_start: 0.8070 (p90) cc_final: 0.7854 (p90) REVERT: H 206 VAL cc_start: 0.9281 (t) cc_final: 0.9002 (m) REVERT: H 218 LYS cc_start: 0.9010 (mttt) cc_final: 0.8734 (mmtt) REVERT: L 4 MET cc_start: 0.9182 (mpp) cc_final: 0.8737 (mpp) REVERT: L 48 ILE cc_start: 0.9283 (mt) cc_final: 0.8918 (tt) REVERT: L 94 TRP cc_start: 0.7783 (t-100) cc_final: 0.7146 (t60) REVERT: L 114 SER cc_start: 0.8286 (t) cc_final: 0.7996 (m) REVERT: L 169 LYS cc_start: 0.9713 (mmmt) cc_final: 0.8947 (tmtt) REVERT: L 175 LEU cc_start: 0.9243 (tp) cc_final: 0.8933 (tp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1835 time to fit residues: 24.5412 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 : 0.957 ------------------------------------------------------------------------------- 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: 5.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** 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 = 0.3564 r_free = 0.3564 target = 0.069969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052378 restraints weight = 120120.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054953 restraints weight = 68615.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.056797 restraints weight = 45419.923| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 8449 Z= 0.288 Angle : 0.756 14.819 11514 Z= 0.396 Chirality : 0.047 0.203 1290 Planarity : 0.005 0.069 1490 Dihedral : 5.991 38.751 1159 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.96 % Favored : 89.85 % 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: -2.09 (0.25), residues: 1059 helix: -2.66 (0.55), residues: 58 sheet: -0.94 (0.29), residues: 312 loop : -1.54 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 353 HIS 0.009 0.002 HIS H 208 PHE 0.026 0.002 PHE H 108 TYR 0.027 0.002 TYR H 33 ARG 0.009 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 84 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.9225 (pt) cc_final: 0.8929 (tp) REVERT: A 392 PHE cc_start: 0.7638 (m-80) cc_final: 0.6852 (m-80) REVERT: A 398 ASP cc_start: 0.8650 (m-30) cc_final: 0.8446 (m-30) REVERT: H 36 TRP cc_start: 0.8564 (m100) cc_final: 0.6766 (m100) REVERT: H 46 GLU cc_start: 0.8894 (tt0) cc_final: 0.8256 (tt0) REVERT: H 218 LYS cc_start: 0.9015 (mttt) cc_final: 0.8723 (mmtt) REVERT: L 4 MET cc_start: 0.9120 (mpp) cc_final: 0.8879 (mpp) REVERT: L 48 ILE cc_start: 0.9334 (mt) cc_final: 0.9081 (mm) REVERT: L 114 SER cc_start: 0.8303 (t) cc_final: 0.8022 (m) REVERT: L 169 LYS cc_start: 0.9748 (mmmt) cc_final: 0.9009 (tmtt) REVERT: L 175 LEU cc_start: 0.9360 (tp) cc_final: 0.9028 (tp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1861 time to fit residues: 22.9887 Evaluate side-chains 57 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 0.4980 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 149 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.072559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053840 restraints weight = 154968.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.056819 restraints weight = 82481.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.058966 restraints weight = 52744.004| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8449 Z= 0.199 Angle : 0.702 15.384 11514 Z= 0.364 Chirality : 0.047 0.184 1290 Planarity : 0.005 0.066 1490 Dihedral : 5.580 36.948 1159 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.25 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.94 (0.25), residues: 1059 helix: -2.69 (0.52), residues: 58 sheet: -0.71 (0.29), residues: 330 loop : -1.49 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 353 HIS 0.010 0.001 HIS H 208 PHE 0.024 0.002 PHE H 108 TYR 0.024 0.002 TYR H 33 ARG 0.006 0.001 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.08 seconds wall clock time: 62 minutes 59.53 seconds (3779.53 seconds total)